Diego Simeone's had to come from behind to gain the point that saw them crowned champions of Spain on a dramatic final day of the season at Camp Nou.
Their 1-1 home draw against Malaga last week forced the title race to a thrilling conclusion, with Simeone's side set to claim the league with a win or a draw - but Barcelona still able to defend their crown with victory.
Atletico were rocked inside the first 25 minutes when injuries forced star striker Diego Costa (hamstring) and midfielder Arda Turan (pelvis) from the field.
Costa was a pre-match doubt due to a hamstring problem, and the decision to risk him backfired for Simeone.
And Barcelona had every reason to feel confident at half-time after Alexis Sanchez gave them the lead with a stunning goal in the 34th minute.
Alexis' strike, which arrowed into the top-right corner from a highly unlikely angle, came after Lionel Messi chested down Cesc Fabregas' lobbed ball.
But sloppy marking from a corner ultimately cost Barcelona, who allowed Diego Godin to steal in unmarked and head in the all-important equaliser four minutes into the second half.
Barcelona thought they had taken the lead when Messi volleyed in from close range during the second half, but his strike was ruled out for offside.
And they were ultimately denied by Atleti's typically stubborn defence as the visitors ended their Liga drought.
The manner of Atletico's win – and their season – saw them applauded by the Barcelona fans after the final whistle had blown.
Meanwhile, Real defeated Espanyol 3-1 but had their triumph overshadowed by a double injury blow ahead of their UEFA Champions League final against Atletico next week.
A Gareth Bale strike and late double from Alvaro Morata proved to be enough for hosts Real in their final game of the domestic season, despite Pizzi's consolation for Espanyol, but the victory was marred by setbacks to Cristiano Ronaldo and Karim Benzema.
Ronaldo, battling a muscle injury in recent weeks, was injured in the warm-up and replaced in the side by Isco.
That puts his involvement in the final of Europe's premier club competition under question, and Real could also be without Benzema after he came off midway through the second half with an apparent groin complaint.
Real dominated the match and ensured victory with a late flurry from Morata – who replaced Benzema off the bench – but the focus will firmly be on the prospects of their injured duo.
