Barca defeated by the better team
Antoine Griezmann's first half header saw Atleti lead for much of the game, something that suited them as a 1-0 scoreline would have seen them advance on away goals.
This resulted in Barcelona throwing the kitchen sink at their opponents, leaving themselves exposed at the back, something that Diego Simeone's men took advantage of to win a late penalty. Griezmann converted, his second of the night.
There was late controversy as Barcelona won a free-kick right on the edge of the area for handball, with replays concluding that the contact was actually a touch inside the penalty area. They missed from the set-piece, and once again the current holders fail to retain their Champions League title.
The start of the game was very different to the closing stages, as Atletico knew they had to score in order to progress, and so came at the Catalans with their attacking talents - often unfairly overshadowed by the team's amazing defence.
Griezmann was always the biggest threat
Star of the night, Griezmann, was buzzing around from the outset, flicking a header into the grateful arms of Marc-Andre ter Stegen after getting on the end of a near post cross.
That wasn't all the hosts were doing going forward, either, as Yannick Ferreira Carrasco was seemingly brought down by Gerard Pique's outstretched leg in the area, only to be denied a penalty.
Barcelona were enjoying more of the ball, with Luis Suarez and Neymar the two looking most likely to make something happen. They didn't though, Griezmann capitalising on that to head Atletico in front, 10 minutes shy of half time.
Much of the credit for the goal has to go to Saul Niguez, who provided the assist. With the ball falling to him on the right hand side, he arched in a perfect cross with the outside of his left foot. Despite the outstanding technique, 5ft 9" Griezmann still had much work to do with the header, nodding it past ter Stegen and into the corner.
It could have got worse for Barcelona before half-time, as Diego Godin made a meal out of a challenge from Suarez, but the referee wasn't convinced by his acting and the striker remained unbooked.
MSN fail to put a dent in Atleti's backline
Ahead on the night, and on away goals, the home side were only too happy to drop back into their favoured counter attacking style, playing a deep line to frustrate Barca even more as the game entered the second half.
It could have been 2-0 just minutes after the restart, Atletico hitting the bar from a corner. Lucas' looping header from that corner wasn't as good a chance as Griezmann had a few minutes later, using his pace to burst down the right hand side, only for a weak effort to be comfortably saved.
Luis Enrique's side looked short of ideas, but did look like they were beginning to turn the screw as the game entered it's final period. It took a brilliant block from Koke to deflect a Messi shot out for a corne just short of the hour mark, the origin of the Catalan's best phase of the game.
Atletico's defence were fantastic all night, but it was Gabi who produced the most impressive bit of individual brilliance. With Jordi Alba emerging in an unfamiliar right wing position, he slid a low ball across goal into the direct of Pique, who had a tap in - or at least he thought he did, only for Gabi to throw himself in front of the ball and poke the ball away from danger.
Griezmann's second sparks wild celebrations
It was those rare chances that the visitors would live to regret, never more so than when they gave away a penalty in the final few minutes.
Throwing virtually every outfielder into the penalty area, Atletico broke perfectly with left-back Filipe Luis. The Brazilian nutmegged one man, holding the ball until the perfect time to set up Griezmann, only for Andres Iniesta to throw a desparate arm at the ball. Penalty given.
Somehow, Iniesta escaped with just a yellow card, but could only watch on as Griezmann put the penalty right into ter Stegen's bottom left hand corner, sparking wild scenes in Madrid.
Barca on the wrong end of late controversy, but deservedly out
Although the home celebrations indicated that the Frenchman's penalty had decided the tie, Barcelona knew that they only needed one goal to force the game into extra time, and six minutes of stoppage time to do so.
They could, and possibly should, have forced extra time. Messi dribbled through the middle of the pitch, sliding the ball to Iniesta five yards to his left. The midfielder jinked inside and took the shot on, with the ball clearly striking the hand of Gabi. However, with the midfielder right on the edge of the 18 yard box, he got away with onl conceding a free-kick, which Messi struck wide.
Barcelona's quarter final curse against Atletico struck again. Simeone has only beaten Barca twice during his time at the club, both in Champions League last eight tie's. The last time they did it, the Madrid club reached the final, and they'll be hoping to do the same this year.