Atalanta came into the game off the back of six wins and had been unbeaten in nine games.
The visitors came into the game off the back of six wins and had been unbeaten in nine games, while Juventus had lost 3-1 at Genoa last week.
The first goal was a neat left-footed shot from Alex Sandro on 15 minutes, and the Brazilian player then revealed a t-shirt in memory of the Chapecoense team who perished in a plane crash in Colombia earlier this week.
Daniele Rugani's powerful header made it 2-0 just four minutes later.
In the second half, veteran Croat striker Mario Mandzukic headed home just after the hour to seal the three points, while Remo Freuler replied for Atalanta eight minutes from time.
The result came as a relief to coach Massimiliano Allegri, whose side host Dinamo Zagreb Wednesday in the last of the Champions League group phase games.
Juventus, beaten finalists two years ago, need a win to remain clear of Sevilla, who they lead by a point in Group H.
On Friday, Napoli beat Inter Milan 3-0 at the San Paulo to climb to fifth place on 28 points.
Napoli star midfielder Marek Hamsik set his sights on Diego Maradona's record haul of 115 goals for Napoli after hitting his 104th goal for the southerners in the win.