Porto were not without their chances either, but they lacked a killer instinct in front of goal, missing a penalty and hitting the woodwork four times on their way out of the competition.
Here, Sports Mole takes an in-depth look at an action-packed night in the Spanish capital.
On target 3
On target 2
Was the result fair?
In terms of the whole balance of play, no. You'd have to say that Porto deserved at least a draw as they dominated possession for large periods of the match and created plenty of chances. However, it is also hard to say that the visitors deserved to win this match as they didn't make the most of the opportunities they carved out. A 2-0 defeat is quite harsh on them but the difference between the two sides was simply that one team finished their chances and the other couldn't. Porto could have won this match with the chances they had, but the fact that they didn't is entirely their own fault.
It wasn't their most stunning performance of the season, but in many ways that makes it even more impressive. They rested a number of players who would normally be in the first team and still managed to beat a team of Porto's quality by two goals. Atletico have thrust themselves into the mix of the La Liga title race, and they should be taken as serious contenders for the Champions League too. They will be a tough nut for any team in the competition to crack and their recent form will have them believing that they can beat anyone. They certainly rode their luck at times this evening, but five wins and a draw from six games in the group stages is a record that has to be respected.
It is hard to evaluate Porto's performance this evening. On the one hand, they were dominant at times against a side who have not lost at home this season and are in sparkling form, but on the other they were terribly wasteful in front of goal. They could have feasibly scored four or five in the first half, while they began the second in a similar vein. Lady luck was not on their side, as four shots against the woodwork shows, but more clinical finishing - as well as a better penalty - may well have given them the three goals they required to progress. They were architects of their own downfall this evening.
Sports Mole's man of the match
Raul Garcia: It was a strange game this evening, which makes the man of the match award tough to choose. However, Raul Garcia gets it if only for the opening goal. The attacking midfielder took the ball down inside the box, rolled his man and smashed his shot in off the underside of the bar from what looked like an impossible angle. The keeper was beaten at his near post but could do nothing about it as the ball was past him before he could move. It was an unstoppable strike.
This one has to go to Josue, who missed a penalty at a vital time in the match. The award of the penalty was slightly controversial, but Aranzubia made sure that his side could have no complaints when he threw himself to his left to make the save. Josue hit it with plenty of power, but it was not a good penalty as it was a nice height for the keeper as well as being fairly central. That miss came when the score was 1-0 and could have completely changed the match for the visitors.
Deniz Aytekin seemed to be on a bit of a power trip at times this evening, handing out yellow cards for fun. There were a few occasions when the German had no option but to brandish a card, but he set the tone early with a needless yellow after just seven minutes and gave out far more than was required. The penalty decision could have gone either way - replays seem to support both sides of the argument depending on what angle is shown - so he can't be criticised for that, but he was so liberal with his cards that it was surprising to see 22 players still on the pitch at the final whistle.
Atletico Madrid: Atletico will look to keep up their title challenge when they face Valencia on Sunday.
Porto: Porto will also be looking to move to the summit of the league table as they travel to face Rio Ave, also on Sunday.