Zenit, who lost the first leg 4-2, opened the scoring after 16 minutes with a brilliant strike from range by Hulk, but the hosts were level near the end of the half through Sebastian Kehl's header.
In an even second half Jose Rondon scored inside the final 20 minutes to set up a nervy finish for the hosts, but Dortmund were able to hold on to qualify for the next round.
Read how the action unfolded below.
6.47pmHello football fans! The Champions League continues this evening with another four teams hoping to get into the quarter-finals. Tonight I have Dortmund against Zenit for you in a game that requires a huge upset from the Russian side if they are to overturn their 4-2 deficit.
6.50pmOf course, this is the Champions League and anything can happen, but Klopp will be delighted with his side's clinical edge three weeks ago and is surely quietly confident of his team's progress. Andre Villas-Boas will not be in charge after being appointed yesterday but will want to see a good performance from his new charges.
6.54pmIt's a big night too for David Moyes, whose Manchester United side take on Olympiacos in tonight's other game. United are 2-0 down from the first leg so still have a chance but will have to improve if there isn't to be an upset at Old Trafford. There is talk of him losing his job if they are knocked out, too. You can follow updates from that game with us right here.
6.57pmWe have the team news in, so let's take a look at who's playing, shall we?
7.07pmA fantastic shot there of a fantastic stadium more than fitting of Champions League nights. Klopp has named about as strong a side as he can, but there are some injuries that ensure it is not as competitive as it might be. As well as the long-term absentee Jakub Blaszczykowski there is no Marco Reus, Sven Bender or Ilkay Gundogan. Four definite first-teamers is fit.
7.10pmEven without those players, though, this is an exciting and attacking lineup. Robert Lewandowski leads the line ahead of Henrikh Mkhitaryan, Pierre-Emerick Aubameyang and the always impressive Kevin Grosskreutz. The German has played more this season than he might have otherwise, but at the moment is undroppable for his recent performances.
7.13pmZenit subs: Lodygin, Luis Neto, Smolnikov, Lukovic, Zyryanov, Tymoshchuk, Rondon
7.16pmAs you can see from the Dortmund subs, Klopp is really scraping the barrel of his squad with the current injuries. Aside from Julian Schieber and Manuel Friedrich all the outfield players on the bench are from the youth team.
7.20pmFor Zenit, caretaker boss Semak has been able to name a near full-strength team, and he will need is as they look to overturn the big deficit. The attacking trio of Aleksandr Kerzhakov, Danny and Hulk are certainly capable of changing games, and Axel Witsel is creative from deep, but it still seems a big ask even with their attacking talent.
7.24pmSo with the two teams considered I do think it will be closer than the first leg. Everything went right for Dortmund that night and it may not again, but they should still have enough to take the win. It might be by one goal but I certainly do not anticipate Zenit getting any further in this season's Champions League.
7.29pmDortmund's league form did start to pick up after a difficult time of things in January and December, but the weekend defeat to Borussia Monchengladbach, despite having an extra man, will be a sour taste for Klopp. His side are certainly fallible, and Zenit will surely look to that result to provide encouragement.
7.35pmThat statistic is another that will offer hope to the away team tonight. It is perhaps a little misleading as Dortmund are so effective on the break that they do not waste any time passing it about, but it does suggest that with the players they have Zenit could take control of the midfield. Sebastian Kehl, as the more defensive of Dortmund's midfield two has an important role tonight.
7.38pmA quick look at the odds shows that the bookies are also not expecting too much from Zenit tonight. To win in the 90 minutes Dortmund are quite strong favourites at 4/11, while the Russian side are some way back at 8/1 in places. The draw, at 4/1, is well worth considering if you ask me.
7.41pmPREDICTION: And since you are asking me, I'll let you know what I think about the result. I've said the draw is good value at 4/1, and key for them is not to lose, so I'm going for 1-1. Zenit could well score the first goal, but the hosts should have enough to get through here.
7.43pmThere's nothing in football quite like a Champions League night. Cool evenings in stadia of European giants with a crowd always in good voice. We're almost ready to go here.
1 minKICKOFF: We are indeed underway then. Dortmund are in their typical yellow, with Zenit in blue. The hosts are straight into their opponents with their gegenpressing.
3 minThe yellow wall is in full voice already and there's a fantastic atmosphere here in Signal Iduna Park. It has been quite a scrappy start as both sides have not yet got on top of the midfield. A good battle in the centre of the park so far, though.
5 minCHANCE! Oh dear Aubameyang! The Gabonese initially wins the ball, before it's played back to Hummels. The centre-back strides forward and finds Schmelzer to his left, who crosses for Aubameyang but from about four yards out he heads wide! Incredible miss, that. It really should be 1-0.
7 minSAVE! First effort at goal there for the away side. Witsel is not closed down quickly enough on the edge of the box and shoots low and hard, but Weidenfeller is down to parry before just getting to the rebound.
10 minZenit have started really well here and are attacking with purpose. It's even overall, but the Russian side have made it clear in the opening 10 that they don't think this is over yet. Dortmund earn the first corner of the game here.
12 minCHANCE! An opening there for Lewandowski. It's nice work on the edge of the box between Mkhitaryan and Aubameyang, before the former plays left to the striker. He lets it run past him and shoots left-footed on the turn but it's a comfortable save for Malafeev. Really good start to this match.
14 minDecent spell of possession in the middle of the park for Zenit, but they're not getting anywhere with it at the moment. Hulk there is guilty of trying an intricate flick from Witsel's pass, but can only find a yellow shirt.
16 minOh my word what can you say?! Hulk was frustrating a few moments ago but that is out of the very top draw. He cuts across from the left around two men before finding the top corner from 30 yards, bending it away from Weidenfeller. That has made it interesting, and that is world class from Hulk!
18 minBOOKING! Lewandowski goes up to meet a corner but ends up handballing it and going into the book. Replays suggest that he might have been pushed, but either way he will now miss the next game. Could be a huge yellow, that.
21 minZenit are really fired up for this now. They're a completely different team to the one that they were in the first leg. Of course, they need another two goals to get through as it stands but the way Dortmund are passing at the moment you wouldn't put it past the Russian side.
22 minSAVE! One for the cameras there from Malafeev there. Grosskreutz tries to wrap his foot around it from around 25 yards, but it's a bit too close to the keeper who flies to tip it over. If that was more in the corner it would have troubled Malafeev.
23 minBOOKING: Second yellow card quickly follows, as Nicolas Lombaerts completely mistimes a tackle and brings down Aubameyang. Hummels glances the header wide from the free kick.
25 minUPDATE: Huge goal at Old Trafford as Robin van Persie tucks in a penalty to halve the deficit. It's 1-0 on the night and 2-1 to Olympiacos on aggregate there. Everything still to play for.
28 minDortmund still haven't got going again since the goal. There were plenty of chances at both ends in the opening exchanges and they've died down just a little lately. It's an important phase of this game - if Dortmund score they'll surely be through.
31 minZenit are working really hard at the back at the moment to limit the threat of Lewandowski and Mkhitaryan in particular. The creativity has been nullified in the last 10 minutes and the away side are just edging on top of things in the last few.
34 minNuri Sahin has a good chance from around 20 yards from a free kick, but drives it straight at the face of one of the players in the wall. The follow-up from range by Kehl is also blocked and Zenit escape. Dortmund are suddenly closing down really well again, but their passing is off.
37 minCLOSE! Zenit are having quite a bit of joy down the left hand side at the moment, with Shatov in particular dangerous. This time he's found in the box and drills a low, hard shot across the face of goal and not far wide of the far post. The Russians have certainly been on top since the goal.
38 minI think Malafeev could have kept that out, but the hosts won't mind. Schmelzer again crosses from deep, and the skipper Kehl makes a brilliant late run to meet it. He heads down and Malafeev gets both hands on it but can only push into the roof of the net. That goal now means that Zenit once again need three - that could be too much to ask now.
42 minLewandowski is clattered by Malafeev in a quite bizarre piece of goalkeeping. Malafeev had a defender able to tackle the Dortmund man, but he goes for it himself and clatters his man. Nothing is given, though. Just a few minutes to play in the half.
45 minAlmost a chance there for Zenit. Hulk first plays a one-two with Kerzhakov, but his attempted cross is deflected up into the air. Kerzhakov tries to volley, but it's nodded away from him towards Weidenfeller, who just gets there ahead of Shatov. Just one minute to be added on.
45+1 minHALF-TIME: Borussia Dortmund 1-1 Zenit St Petersburg
8.33pmFor a while Zenit were right back in this tie, but that's the danger of conceding four goals at home - one from Dortmund has made sure that the Russians need three more unanswered to claim a win.
8.37pmThe Hulk goal on 16 minutes completely lifted the away team. It was soft defending to let him cut inside but the strike from 30 yards was absolutely magnificent. Kehl, however, came to his side's rescue and Malafeev will be very disappointed having let it in.
8.41pmAn update from the game at Old Trafford: Van Persie added his second on the stroke of half time to send United in at 2-0 and Moyes in very happy. It's 2-2 on aggregate now and United will be the heavy favourites to qualify.
8.45pmIt won't be long now until the second half. Can Zenit pull a rabbit out of the hat in the second 45? I can't see it, but they certainly have the players capable of scoring three goals. Will they manage not to concede again? I'm less convinced of that.
46 minWe're back underway here then with the hosts kicking things off. At the break Lombaerts has made way for Luis Neto.
49 minDortmund are well in control of the early stages of this half. They're passing the ball around patiently in the midfield, but have not managed to create a chance as yet. Zenit are chasing shadows at the moment.
50 minFantastic cross there from Witsel on the right. He was sent clear and did get his cross into a dangerous area but it managed to miss all three of his teammates who had burst into the box.
52 minDecent enough strike from Hulk from a free kick around 35 yards from goal, but it was always rising over the crossbar. Neat football between Kehl, Mkhitaryan and Aubameyang before the latter is tackled for a corner.
53 minUPDATE: A third goal at Old Trafford and it's also a third for Van Persie. United are 3-0 up on the night and 3-2 up on aggregate. The turnaround is complete, will they now go for the kill?
56 minWhat a waste that is from Kerzhakov! He has Hulk to his right in a very dangerous position, but puts it straight out for a goal kick. That could have been a chance. The Zenit fans are still in excellent voice here.
59 minAubameyang has not had many sights of goal since his early header, but he has just shot from about 25 yards. However, his strike flies over the bar and wasn't close to finding the net in truth.
62 minZENIT SUB: Last action of the game from Kerzhakov as he's replaced by Jose Rondon. Under 30 minutes now for those three Zenit goals and they are not having many sights either.
65 minStill Dortmund with most of the passing in this one, but there have been very few chances in this half. Lewandowski is looking more and more frustrated and has just gone down very unusually - he threw himself backwards after a minor coming together with Neto.
68 minSome good football from the hosts to the right side of the box, but the eventual cross from Sahin goes out of play. Mkhitaryan, who has worked hard, makes way for young Milos Jojic, who scored at the weekend.
71 minThe Russian side do seem to have run out of ideas. It's one-way traffic now from Dortmund as we move into the final 20 minutes. This would be a monumental comeback if they were to do it now.
73 minI spoke too soon. Zenit edge ahead on the night again and it's the sub Rondon. Hulk found Criscito, who clipped in a low cross for Rondon to get ahead of Hummels and send a stooping header into the net. Two goals needed for them now...
75 minBOOKING: Jojic goes into the book for a really poor late tackle on Witsel. Absolutely right to be carded, there.
78 minLewandowski again hits the deck, but this time he was genuinely caught. Dortmund have plenty of players back at the moment, just in case. They do still look like the most threatening side going forward, however. Zenit just have to throw the kitchen sink at them now.
81 minDortmund are trying to slow things down now with the two-goal cushion that they currently have. They've created absolutely nothing in the final third, though, in this half and Zenit still look most likely to score even if they aren't seeing as much of the ball.
84 minTime is very quickly running out for Zenit, but whatever happens now AVB will be pleased with what he has seen from the team he will soon take over.
86 minHulk is a bit unlucky there to concede a foul in what was not much more than a shoulder challenge against Piszczek. It's another free kick that will run the clock down for the hosts and it's getting really scrappy.
88 minCLOSE! Really good low strike from around 25-30 yards from Witsel. I'm not sure it was sneaking in but Weidenfeller has to tip it around the post anyway.
90 minPowerful shot from Shatov as he skipped inside a challenge, but it was straight at Weidenfeller, fortunately enough for the home goalkeeper. Ouch! A lot of blood here on the face of Hubochan who took a knee right in the face from Lewandowski. Aubameyang is off for Jonas Hofmann.
90+1 minThere will be three minutes of time to be added on as Hubochan, with head bandage, is desperate to get back on.
9.37pmWell, that was a lot more tough than it should have been for the German side, but they have just about done enough to qualify for the quarter-finals. They were beaten on the night but are through 5-4 on aggregate.
9.38pmThat's all we have time for from this one tonight. Thanks for joining me and please do stick around on site for reports and reaction from tonight's action. Goodbye.