Marco Parolo gave the home side an early lead but goals from Duvan Zapata, Timothy Castagne and an own goal by Wallace saw Gian Piero Gasperini's side complete a comeback.
The Bergamo side are fourth on 62 points but have moved within one point of third-placed Inter Milan, who were held to a goalless draw by Udinese on Saturday.
Lazio, who will face Atalanta again in the Coppa Italia final on May 15, are now seven points adrift of the top four in eighth place with three rounds remaining.
Parolo rolled a shot into the bottom corner after just three minutes but Zapata equalised with a composed finish midway through the first half.
It was the Colombian’s 22nd league goal of the campaign, the most any Atalanta player has scored in a single Serie A season since Filippo Inzaghi struck 24 times in 1996-97.
After the break Papu Gomez intercepted a slack pass from Wallace before teeing up Castagne’s finish. The win was secured when Wallace rose to head into his own net from a corner.
Roma, in fifth place, can narrow the gap with Atalanta to one point by beating Genoa later on Sunday, while AC Milan can move within three points of the top four by winning against Bologna on Monday.
Elsewhere, Frosinone’s relegation was mathematically assured when they surrendered a two-goal lead to draw 2-2 at Sassuolo, while 18th-placed Empoli moved within two points of safety with a 1-0 Tuscan derby win over Fiorentina.
Sampdoria striker Fabio Quagliarella scored a brace in his side’s 3-3 draw with Parma to move three goals clear at the top of the Serie A scoring charts with 25 strikes.
(Reporting by Alasdair Mackenzie, editing by Pritha Sarkar)
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