A double from Giacomo Bonaventura sealed an unlikely victory for Stefano Colantuono's side, who had spent much of the second half sitting back and repelling a mis-firing Inter side. Mauro Icardi had drawn the sides level, before the Orobici provided the late sting in the tail. Inter have now failed to beat Atalanta home or away since April 2010.
Inter named an unchanged side from the one that defeated Hellas Verona 2-0 last weekend, while Atalanta were forced into one change from the eleven that swept past Sampdoria. Constantin Nica came into the defence in place of the suspended Yohan Benalouane.
Hernanes was the early architect for the Nerazzurri. The Brazilian ghosted past his markers to create two chances for Fredy Guarin, but both efforts were off target.
Atalanta were just as dangerous, and Inter had Samir Handanovic to thank for keeping them out. The shotstopper palmed away from Guglielmo Stendardo in the box, then beat away a Luca Cigarini sweeping volley after German Denis teed him up.
Handanovic was rooted to the spot and could only watch as Denis's 17th minute header clipped the top of the crossbar.
Andrea Consigli showed safe hands to smother a Guarin effort, then ran out to close the angle on Icardi by the touchline. The Argentine was in two minds whether to go for goal or roll across the box where an unmarked Rodrigo Palacio was waiting to pounce, but Consigli made the block with his legs.
Bonaventura saw Handanovic off his line and his long range effort just dipped inches over the bar. The Atalanta man went one better with his next effort, opening the scoring for the visitors ten minutes before the break. Maxi Moralez went on the counter attack from deep in his own half and picked out his teammate to blast through a sea of players from the edge of the box.
Inter were back on level terms less than 60 seconds later. Guarin's through ball released Icardi, who cut inside Mario Yepes and fired a low shot past Consigli. Icardi held up a t-shirt declaring his love for girlfriend Wanda Nara, who is the ex-wife of the striker's former Sampdoria teammate Maxi Lopez.
Atalanta lost Moralez to a calf injury seven minutes before the break. On the stroke of half time, Danilo D'Ambrosio crept towards the far post and sent a low shot wide.
Inter dominated the second half and looked most likely to get the decisive third goal. Jonathan's angled drive forced Consigli into a low save, while Cristiano Del Grosso deflected Guarin's effort wide.
The home side hit the woodwork twice in succession. Guarin rattled the crossbar from distance, before Palacio's glancing header on the hour mark bounced off the post.
Walter Mazzarri made attacking changes and Atalanta retreated. Eight minutes from the end, the defence sat back and allowed Ricky Alvarez to fire high and wide from outside the D.
Atalanta stirred and almost went ahead three minutes from the end. Substitute Daniele Baselli dribbled past the Inter defence and pulled back from the byline, Denis left it and Franco Brienza's shot was cleared by Jonathan's last ditch challenge.
Inter went down the other end and really should have scored. Jonathan lifted a shot over Consigli and onto the crossbar, before Cristian Raimondi got a crucial touch to divert Icardi's follow-up wide from the goalmouth.
Atalanta punished their wasteful hosts in the final minute. An unmarked Bonaventura got on the end of a free kick to powerfully head the ball down and underneath Handanovic's legs.
Yuto Nagatomo had one final chance for Inter, but the substitute's indecisiveness saw the ball get cleared.
Inter Milan: Handanovic; Campagnaro, (Kovacic 82) Ranocchia, Rolando; Jonathan, Guarin, Cambiasso, (Alvarez 61) Hernanes, D'Ambrosio; (Nagatomo 71) Palacio, Icardi
Goals: Icardi 36
Atalanta: Consigli; Nica, (Raimondi 75) Stendardo, Yepes, Del Grosso; Estigarribia, Cigarini, (Baselli 86) Carmona, Bonaventura; Maxi Moralez; (Brienza 38) Denis
Goals: Bonaventura 35, 90