Giacomo Bonaventura gave Atalanta an early lead which lasted until 11 minutes into the second half when Fredy Guarin equalised.
German Denis restored Atalanta's lead instantly before adding a third from the penalty spot in the 67th minute.
Rodrigo Palacio brought Inter back into the game in the 84th minute and Atalanta were reduced to 10 men when Facundo Parra was dismissed in stoppage time, but the Bergamese side held on to the points to move up to sixth in the table.
Sunday afternoon's big game saw Lazio inflict a third straight 'Derby della Capitale' defeat on Roma as Stefano Mauri's goal edged a 3-2 victory as both sides were reduced to 10 men.
Erik Lamela temporarily lifted the Giallorossi above their fiercest rivals in the league table, opening the scoring with a confident header at the Stadio Olimpico.
But Vladimir Petkovic's Lazio soon seized control and Antonio Candreva and Miroslav Klose turned the tables on Roma before half-time.
Daniele De Rossi was sent off for punching Mauri in first-half stoppage time and his victim sealed the win after the restart.
But the Lazio captain was eventually sent off for handball, allowing Miralem Pjanic to reduce the deficit from a bizarre free-kick.
AC Milan's mini-revival came to an abrupt end as Fiorentina beat Massimiliano Allegri's hapless side 3-1 at the San Siro.
Alexandre Pato failed to peg La Viola back before the break as he missed a penalty following Alberto Aquilani's opener.
Borja Valero gave Fiorentina a two-goal lead but substitute Giampaolo Pazzini hit back to give Milan hope, only for Mounir El Hamdaoui to make the visitors' points safe at the death.
Napoli remain in the hunt for the Scudetto after rallying to a 4-2 win at Genoa.
Walter Mazzarri's side came from behind twice before finding two late goals to clinch all three points at the Stadio Luigi Ferraris.
Ciro Immobile put Genoa in front but former Grifone defender Giandomenico Mesto levelled early in the second half.
Andrea Bertolacci restored Genoa's lead almost immediately before Edinson Cavani brought Napoli level again with just over 10 minutes to go.
Marek Hamsik put Napoli in front for the first time in the last minute, before Insigne completed the win with the last kick of the game.
In Sunday's early game, Palermo found a new hero after 18-year-old striker Paulo Dybala scored his first two goals in Italy to down Sampdoria 2-0 at the Stadio Renzo Barbera.
Gabriele Angella's 91st-minute strike earned a 2-2 draw for Udinese, two minutes after Alberto Paloschi's spot-kick looked to have won it for hosts Chievo.
Elsewhere, Danilo D'Ambrosio scored the only goal of the game as Torino saw off lowly Bologna 1-0, while Parma shared a goalless draw with basement boys Siena.