Vedad Ibisevic opened the scoring after nine minutes, before Werner doubled their lead a minute later.
Read how all the action unfolded below:
4.28pmGood afternoon. With just a couple minutes until kickoff, let's take a quick look at the team news.
4.29pmFREIBURG STARTING XI: Baumann, Diagne, Ginter, Gunter, Hohn, Fernandes, Mehmedi, Coquelin, Hofler, Klaus, Freis
4.30pmSTUTTGART STARTING XI: Ulreich, Schwaab, Haggui, Niedermeier, Rausch, Kvist, Leitner, Werner, Genter, Maxim, Ibisevic
1 minStuttgart get the game underway.
2 minStuttgart are on the attack early and force a corner in absolutely torrential conditions in the Mage Solar Stadion. Maxim tries to volley the ball in, but is being closely marked and can't quite get enough space to make the shot.
5 minHaving been tested in the opening couple of minutes, Freiburg manage to string together a string of passes in their own half, but their struggling to penetrate the Stuttgart defence in the early stages of this match.
8 minCHANCE! A stunning solo effort from Admir Mehmedi creates the first real chance of the match, as the midfielder burst down the wing before taking the ball into the box and lashing it towards the Stuttgart goal, but Ulreich just managed to tip it wide. Ginter gets a chance from the resulting corner, but his finish goes wide.
9 minGOAL! Freiburg 0-1 Stuttgart (Ibisevic)
9 minIt's a superb finish from Vedad Ibisevic to give the visitors an early lead. Gentner plays the ball in for the striker to coolly chip over the keeper. Great start for Stuttgart.
10 minGOAL! Freiburg 0-2 Stuttgart (Werner)
10 minWhat a minute for Stuttgart! Timo Werner wins the ball straight from the restart and bursts into the box before smashing it into the roof of the net. Freiburg look stunned.
13 minCHANCE! Rausch breaks down the right and crosses in for Ibisevic, who only has to make the slightest of touches to add his second in the space of five minutes, but the wet pitch causes him to slip, and he can't quite reach the delivery. This is worrying for Freiburg, it's going to be a long afternoon for the hosts if they don't slow they're opponents down.
16 minFreiburg manage to force the visitors back into their own half, before Ginter looks to find his way into the Stuttgart box. He finds Klaus, but his first touch is poor, and it goes behind for a goal kick.
20 minStuttgart are starting to control the possession, taking their time to play the ball out from the back before stretching their opponents with a series of quick passes in midfield. Werner looks to push forward, but Freiburg are in damage limitation mode, with plenty of men back.
24 minCHANCE! Freiburg win a free kick on the edge of the box, after Klaus was brought down. It's a good opportunity for the home side. Klaus whips it in across the face of goal, and Mehmedi rushes in to try and tap it in, but his times it wrong, bundling the ball behind. It does look like Freiburg have recovered from the shock of Stuttgart's quick-fire goals earlier on.
27 minThere's a bit more urgency from both sides in midfield at the moment. Mehmedi's effort has clearly given the hosts a boost. Ibisevic looks to create a third for Stuttgart as Gentner launches the ball forward, but the striker can't get control in time.
28 minBOOKING! Felix Klaus is booked for a loose challenge on Werner. The foul also gives the visitors a free kick from around 25 yards out, but it comes to nothing.
31 minOFFISIDE! Werner is on the attack again, but Freiburg manage to turn the ball behind for a Stuttgart corner. It's initially cleared before Gentner sends it back in for Werner, but the second goalscorer is flagged offside, although he played on and put it in the back of the net anyway for a bit of target practice.
33 minThere's an injury concern for Freiburg as Gelson Fernandes appears to have picked up an ankle knock, but it looks like he'll try to play on form now.
35 minCHANCE! Rausch has a rather hopeful shot from 25 yards out, drilling it in low but with no real power behind the effort, giving Baumann an easy stop.
38 minFernandes seems to have shaken off his earlier ankle problem, but does earn himself a talking to from the referee and sliding in two-footed on Niedermeier.
40 minPENALTY APPEAL! Freiburg look to the referee for a penalty as Hofler is brought down by Haggui. The Stuttgart defender got the ball first though, and was only carried into the midfielder because of the wet playing surface, so the shouts are waved away.
42 minHofler looks to apply more pressure inside the box as Freiburg are enjoying their first prolonged spell of pressure inside the Stuttgart half, but he's blocked by Schwaab.
44 minBOOKING! Georg Niedermeier is shown a yellow card for a two-footed challenge from behind on Klaus.
45 minHALF TIME: Freiburg 0-2 Stuttgart
5.18pmStuttgart have a two-goal lead over Freiburg at half time, having netted twice in the space of a minute early on. The home side managed to weather the storm though, and created some good chances just before half time. A goal early in the second half would get Freiburg right back in this match.
5.23pmLet's take a look at some of the stats from the first half. The teams shared possession 50-50. Stuttgart had six shots with four an target, while Freiburg had four, with just the one testing Sven Ulreich. Both sides had one player booked in the opening 45 minutes.
5.27pmWhile Vedad Ibisevic has looked threatening in front of goal, Timo Werner has been the big problem for the home side so far, showing blistering pace and flashy footwork in midfield, while proving his shooting credentials with the second goal. Freiburg will need to find a way to stop the teenager in the second half if they're to get back into this match.
5.29pmFelix Klaus and Admir Mehmedi have linked up well to create chances for the hosts, but have lacked the finishing touch. They might look to involve striker Sebastian Freis more when they return for the second half.
5.31pmIt looks like Sebastian Kerk is getting ready to come on for Freiberg at the start of the second half. He's out of his tracksuit in his kit finishing a warm up.
5.32pmSUB! Kerk is indeed coming on, replacing Francis Coquelin, who was pretty anonymous in the first half. The players are heading back out onto the pitch. Freiburg were back out early, but Stuttgart are out now too.
46 minFreiburg kick off the second half.
48 minStuttgart initially win the ball and try to hold on to it among their back four, but Freiburg are keen to continue where they left off in the first half, and try to win it back. Freis manages to pull it back for Kerk before Klaus gets a chance from the edge of the box, but it's blocked by Niedermeier.
50 minStuttgart immediately go on the counter attack, but Maxim loses control of the ball and knocks it behind for a goal kick. The next goal will be crucial, and it looks like both sides have started this half determined to make sure they're the ones that score it.
54 minStuttgart are on the attack with Maxim trying to find a way into the box, but his path is well blocked and he has to go backwards. The visitors chose to slow things down instead, passing it back as far as Ulreich, before Ibisevic plays Werner in, but the teenage playmaker can't quite control it quick enough to get his shot away.
56 minIt looks like the visitors will have to make a change, as Rausch appears to have pulled his hamstring. While down receiving treatment, Werner signals to the bench that they'll need to make a change, so it looks like the right-back's day may be done.
58 minSUB! Rausch does indeed have to make way, as Gotoku Sakai comes on in his place.
59 minCHANCE! Ulreich shows lightening-fast reactions to make a save as Ginter tries to head in from a Kerk free kick. Freiburg have certainly looked a brighter side since the introduction of Kerk at half time.
61 minThe home side win a corner, and Kerk curls it in to Ginter, who has been getting into some strong positions on set pieces this afternoon. There's half an appeal for a penalty as Niedermeier leaves a flailing arm in the box, but manages to move out the way just in time to avoid a hand ball.
63 minSven Ulreich commits a frankly embarrassing dive! The Stuttgart goalkeeper comes under pressure from Gunter while gathering the ball in the box. He picks it up just before the midfielder reaches him, but goes down clutching his face as if the Freiburg man had caught him, but relays show there was no contact. Give that man an Oscar!
67 minIt's all Freiburg at the moment, as the home side continue to press to get back in the match. Haggui concedes a corner, but the visitors make a good clearance. A deep throw from Ulreich finds Ibisevic, but the scorer of the opening goal doesn't have enough space to turn and look for the goal.
72 minFreiburg win a corner, and it drops nicely for Ginter, but Niedermeier manages to get his head in the way to deflect it wide. Kerk delivers the second corner, which is initially cleared before Ulreich manages to keep hold of the ball.
75 minSebastian Freis tries to find the goal from distance, but it goes well high of the crossbar. The home side quickly win the ball back and Mehmedi looks to fire it in, but he can't get the angle right. It looks like Freiburg are starting to get a bit desperate.
78 minGOAL! Freiburg 1-2 Stuttgart (Hanke)
78 minMike Hanke has been on the pitch for just over a minute, and he's got Freiburg right back into this match already! Mehmedi has the ball in the box but sees effort blocked. However, it's only cleared to the edge of the penalty area, where Hanke was waiting, and his smashes it in on the half volley. It's a super strike from the super sub.
81 minSUB! Stuttgart make a second change as they look to hold on to their lead. Leitner comes off, making way for Martin Harnik.
82 minGOAL! Freiburg 1-3 Stuttgart (Werner)
82 minTimo Werner picks up his second goal of the day to surely seal the win for Stuttgart. The home side think they've cleared a Stuttgart corner, but Werner picks it up around 30 yards out, bringing it back to the edge of the box before driving it home. It's been a fantastic day's work from the 17-year-old.
85 minSUB! Werner's work is done! The scorer of two of Stuttgart's goals is replaced by Ibrahima Traore for the last few minutes of this match.
88 minFreiburg aren't sitting back, as Kerk charges towards the Stuttgart penalty area, but play is stopped when Mehmedi collides with Ulreich.
90+1 minCHANCE! Ibisevic beats several defenders before unleashing an effort at the Freiburg goal, but it's well saved. Meanwhile, there are three minutes of stoppage time to be played.
90+3 minBOOKING! Mike Hanke earns himself a late booking for a wild challenge on William Kvist, while also gives the visitors a free kick in a strong position, but it goes just wide.
90+4 minFULL TIME: Freiburg 1-3 Stuttgart
6.22pmSo two goals from Timo Werner help Stuttgart to a 3-1 win over Freiburg. The result lifts the victorious side up to eighth in the Bundesliga table, while Freiburg remain in the relegation playoff berth.
6.23pmThat's all from this match, but stick around to read reports from all of today's games from across Europe. Thanks for joining me this today, goodbye.