Giacomo Bonaventura, who had put Atalanta in front in the first half, scored with a header to give his side a second consecutive away league victory against Inter after they won 4-3 in the San Siro last season.
Fourth-placed Fiorentina boosted their hopes of a Champions League place with a 1-0 win at third-placed Napoli, who played the entire second half with 10 men after Faouzi Ghoulam was sent off for a foul on Marko Bakic in the 37th minute.
Former Spain forward Joaquin Sanchez headed Manuel Pasqual's cross into an empty net with three minutes to play after Napoli goalkeeper Pepe Reina was caught out of position.
The win left Fiorentina seven points behind their opponents, who are in the Champions League playoff spot.
Udinese beat relegation battlers Sassuolo 1-0 after both teams missed penalties and Sampdoria thrashed Verona 5-0, with their second goal coming after the ball struck the referee.
Atalanta went ahead in the 36th minute against Inter when Bonaventura finished off Maxi Moralez's counter-attack, only for Argentine forward Mauro Icardi to equalise one minute later after running on to Fredy Guarin's pass.
Inter dominated the second half as Guarin smashed a long-range effort against the crossbar and Rodrigo Palacio sent a header against the foot of the post.
That was followed by an incredible double miss in the 85th minute when Jonathan's shot rebounded off the bar to Icardi whose point-blank range effort was blocked by a defender and struck the post.
Inter coach Walter Mazzarri was already showing his exasperation on the touchline when Atalanta won a free kick and Bonaventura escaped his marker at the far post to score with a header which went between goalkeeper Samir Handanovic's legs.
Inter were left joint fifth on 47 points with Parma who earlier drew 1-1 at home to Genoa.
Sampdoria, beaten 3-0 at Atalanta last week, replied to some stinging criticism from coach Sinisa Mihajlovic by demolishing Verona with Roberto Soriano scoring twice and Gianluca Sansone, Renan and Angelo Palombo sharing the other goals.
Renan's effort came after a corner was deflected into his path by the referee.
Antonio Di Natale, making a club record 324th Serie A appearance for Udinese, celebrated by putting them ahead in the 26th minute but blotted his performance by firing wide from the penalty spot 10 minutes later.
Sergio Floccari sent a second-half penalty against the post for Sassuolo who were left floundering in the relegation zone.
- Sports & Recreation
- Giacomo Bonaventura
- Mauro Icardi
- Faouzi Ghoulam
- Fredy Guarin