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 possible recurrence of his hamstring injury after manager Tito Vilanova had already made his three substitutions.
The Catalans, left with an unassailable lead at the top of 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.
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 respectively.
The hosts had one eye on Friday's King's Cup final against Real at the Bernabeu but still fielded a near full-strength side, though there were few chances of note in the first half.
Just after the restart Atletico caught the visitors on the counter-attack and despite being on the ground Gabi managed to knock the ball into the path of Falcao who scored.
It was the Colombia striker's 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 a scuffed David 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 by Paris St Germain 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.
Valencia 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 stage.
Real Sociedad slipped to fifth with 58 points before playing their game in hand at home to struggling Granada on Monday.
In the battle for Europa League places Malaga, who host Sevilla later on Sunday, are sixth with 52 points, one point and one place ahead of Real Betis, who beat relegation-threatened Celta Vigo 1-0.
Teams finishing fifth to seventh in La Liga qualify for the Europa League.
Betis had two efforts ruled offside in the opening 10 minutes and had to wait until the 67th before Ruben Castro volleyed the winner, the striker benefiting from a slip by his marker to fire home.
Celta thought they had equalised near the end but the effort was given offside, although replays showed it should have stood, and the 19th-placed Galicians stay deep in the drop zone on 31 points, three short of Real Zaragoza in the last safe spot.
- Sports & Recreation
- David Villa
- Radamel Falcao
- Real Madrid