It was a night of frustration for Juventus as Atalantas goal came after a stoppage time penalty was saved.
But Juve were the better team when it came to defending and in the end it was Juventus who won the game in extra time.
Juventus had the better chances in the first half but the visitors got their first serious chance when Leonardo Bonucci put his foot in the box.
The Atalantes keeper was able to stop the free-kick but the penalty was awarded and Bonucci had to stand up to a challenge from his opponent.
Juventus were given a second opportunity to score after Leonardo Bonetti got a hand on the ball, but it fell to his feet to deny Atalanti striker Paulo Dybala.
The goal came just before the break when Mario Balotelli struck for the second time in the last four minutes and he headed in the rebound to put Juventus on top.
Alessandro Florenzi had an effort from close range blocked but there was no chance for Atalante goalkeeper Federico Crespo to make a save as Juve doubled their lead with another goal from their goal.
The result means Atalentes top-flight record is now eight games without a win and Juve are now nine points adrift of third-placed Juventus in second spot in the table.