Radamel Falcao had threatened to spoil Barca's title party when he struck in the 51st minute, but Alexis Sanchez levelled in the 72nd before David Villa's miscued shot was diverted into his own net by Gabi eight minutes later.
Barca had to play with 10 men for the last 20 minutes after Lionel Messi was forced to leave the pitch with a recurrence of his hamstring injury after coach Tito Vilanova had already made his three substitutions.
The Catalans, left with an unassailable lead in the standings on Saturday when second-placed Real Madrid drew 1-1 at Espanyol, moved 10 points clear at the top on 91.
With three games left, Barca have a chance to match Real's record 100 points tally for a season from last year. Jose Mourinho's side have 81 points but with two matches to play.
"I would like people to value this title for the work done by everyone, and not for the health problems," Vilanova told a news conference referring to his battle against throat cancer and attempts to label their success 'Tito's title'.
"This isn't Tito's title, it is for all the players. They deserve a lot of credit because it is difficult to win when the coach is absent for two months [receiving treatment].
"I didn't watch Real's game last night. I looked at the internet and saw it was 1-1 and went to bed because I was thinking about today's game."
GUARD OF HONOUR
Atletico gave Barca a guard of honour as they entered a festive Calderon stadium, with both teams having achieved their main objectives - the league title and automatic Champions League qualification for a third-placed finish respectively.
The hosts had one eye on Friday's King's Cup final against Real but still fielded a near full-strength side, and just after the restart caught the visitors on a counter-attack when Colombia striker Falcao scored his 28th goal of the season.
Alexis levelled for Barca, after exchanging passes with Cesc Fabregas, as he raced into the area and wrong-footed goalkeeper Thibaut Courtois.
With 10 minutes to go, Gabi was unable to get out of the way of a scuffed Villa shot that was going wide, and the ball went in off his thigh.
Earlier, Roberto Soldado scored twice to keep Valencia in the running for a return to the Champions League next season with a 4-0 victory at Rayo Vallecano.
The Spain striker netted a penalty after 28 minutes and doubled the lead with a simple tap in from Andres Guardado's pass in the 34th, taking his season's league tally to 21.
Mexico midfielder Guardado netted midway through the second half, and Paraguayan substitute Nelson Haedo Valdez lashed a fourth high into the net on a counter-attack.
Valencia were knocked out of Europe's elite club competition at the last 16 stage in March but their hunger for a return far outweighed 10th-placed Rayo's fading hopes of qualifying for the Europa League.
They climbed to fourth on 59 points, and edged ahead in the race for Spain's place in the playoffs for next season's Champions League group st
