There was controversy at the Vicente Calderon as last season's treble winners felt an Atletico handball occurred inside the box, but the referee disagreed.
Barcelona's Champions League exit contained late drama as the club was denied a penalty with two minutes to go that, if scored, could have taken the quarterfinal tie against Atletico Madrid into extra-time.
The European cup holders were 3-2 behind on aggregate - having just conceded a second Antoine Griezmann goal on the night - when Andres Iniesta's shot hit Gabi's arm.
Despite cries from Barca's players that the handball was inside Atletico's 18-yard box, referee Nicola Rizzoli opted to award just a free kick to Luis Enrique's men.