The unbeaten Nerazzurri overtake defending champions Juventus, who again slipped up earlier today as they lost 3-2 against Sampdoria.
A couple of second-half headers from Mauro Icardi, now behind only Ciro Immobile in the scoring charts, were enough for Inter to return to winning ways after being held by Torino here in their last outing.
Atalanta have already taken points off Juve this term and looked good value to do likewise against Inter when heading into the half-time interval all square.
Josip Ilicic sent Hans Hateboer clear for the game's first real shot, which Samir Handanovic was equal to, while Icardi also came close to an opener in the first 45 minutes only to fire right at Etrit Berisha.
Icardi was guilty of squandering a few chances before eventually finding a way through, with that key opener arriving 51 minutes in after getting ahead of Bryan Cristante for a free header.
Papu Gomez perhaps should have levelled up moments later, firing high over the bar from a good position, and it would ultimately prove costly as Icardi met Danilo D'Ambrosio's cross and glanced into the far corner for his second.
Atalanta, beaten 7-1 here the last time these two sides met, searched for a route back into the game in the remaining minutes, but Handanovic thwarted Andrea Petagna and Maarten De Roon was wasteful from 20 yards out.