It was another professional performance from the Serie A leaders, who maintained their 12-year league unbeaten run against the Bergamo club to stay five points clear of Roma.
Juve opened the scoring after just six minutes when Carlos Tevez scored his fourth goal in his last two league games. Atlanta levelled shortly when Maximiliano Moralez became the first Serie A player to score against Gianluigi Buffon in 745 minutes of football.
But any hopes an Atalanta victory were quashed in the second half, with Paul Pogba restoring their advantage just a minute after the break.
And the champions made sure of all three points in the last 15 minutes with goals from Fernando Llorente and Arturo Vidal as their ominous form continued.
Experienced defender Guglielmo Stendardo came into the Atalanta defence as one of three changes from their 1-1 draw with Genoa, while Claudio Marchisio and Stephan Lichtsteiner started for Juve in place of Mauricio Isla and Federico Peluso.
Juve made a bright start and took the lead after just five minutes as Tevez's low strike from the edge of the area snuck past Atalanta goalkeeper Andrea Consigli.
The visitors' lead was short-lived though, as Moralez levelled nine minutes later when he slotted home from close range following good work down the right from Giacomo Bonaventura.
Despite that setback, the Turin outfit continued to dictate the play but they were prevented re-taking the lead on the half-hour mark when Consigli produced a superb stop to keep out a near-post effort from Tevez.
However, just a minute into the second half the champions were back in front thanks to Pogba's neat finish after Llorente had smartly turned Kwadwo Asamoah's left-wing cross into his path.
Atalanta struggled to gain a foothold in the contest and were fortunate not to fall further behind midway through the second period as Tevez's free-kick was deflected narrowly wide of the post.
The pressure from Antonio Conte's told 15 minutes from time, when Spain striker Llorente turned smartly in the area before firing past Consigli and into the bottom corner.
The Turin giants refused to take their foot of the gas and the fourth goal came only four minutes later as Vidal tapped in Lichtsteiner's low delivery to put the gloss on a comfortable win.
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