Carlos Tevez put the Bianconeri in front in the sixth minute but Maximiliano Moralez became the first player in over seven matches to beat Gianluigi Buffon to bring Atalanta level 10 minutes later.
Paul Pogba restored Juve's lead early in the second half with Fernando Llorente and Arturo Vidal completing the win.
Juve have been going - Champions League apart - like an express train recently, winning their last eight and not conceding in their last seven, and Bergamo was not a scheduled stop.
It stood to reason, therefore, that Tevez put them in front with their first attack, netting his 11th goal of the season after only six minutes.
Vidal's pass took a fortunate deflection to fall for the Argentinian, who held off his marker well and shot low from the edge of the area into the bottom left-hand corner.
Their lead lasted less than 10 minutes, though, before Buffon conceded his first goal after 744 minutes.
Giacomo Bonaventura took the ball to the goal-line and pulled it back for Moralez, whose shot towards the far corner took a slight deflection, striking the inside of the post on its way in.
Ten minutes later, Carmona tried his luck from 35 yards, hoping somehow that Buffon could now be beaten from anywhere having finally conceded, yet he failed to hit the target.
Juve ended the half stronger with Claudio Marchisio lifting an interesting ball to the far post to Pogba, who found no takers for his header across the face of goal. Tevez then tried a lob which cleared the bar from the edge of the penalty area.
Less than a minute of the second half had been played when Pogba put Juve in front for the second time.
Kwadwo Asamoah's cross was touched town by Llorente, and Pogba swept it into the far corner with his left foot.
Atalanta collapsed as Juve finally gathered momentum, and a third goal was inevitable.
Giorgio Chiellini was allowed to advance with the ball at his feet, deep into the Atalanta half, where he passed the responsibility to Llorente, who made it look easy inside the penalty area.
Five minutes later, Vidal got his obligatory goal too, tucking the ball in at the far post from Stephan Lichtsteiner's cross to complete the rout.