The Bianconeri were made to work exceedingly hard for their win, and were perhaps fortunate to escape with the points in the end after the home team was denied a late penalty.
The Bianconeri had little left to play for after clinching the Scudetto against Palermo on Sunday, but picked up their ninth straight league win thanks to Alessandro Matri's well-worked first-half goal.
With the title wrapped up over the weekend, Antonio Conte opted to give some of the less-heralded names in his squad a chance to shine, as Marco Storari, Luca Marrone and Simone Padoin all started.
The opening goal came in the 18th minute courtesy of good work from Andrea Pirlo who clipped a sublime pass between the center backs for Matri, who controlled superbly before lashing into the far side.
The goal seemed to coax the home side out of its shell, but it was Juve which nearly struck again less than 10 minutes later. Mauricio Isla’s fantastic cross was begging to be met and Paolo De Ceglie obliged, but his stooping header was just wide.
But just when it seemed like matters on the pitch were picking up, events in the stands ground proceedings to a halt. Flares and smoke bombs were thrown, forcing the referee to stop the game, with Conte and Juve defender Giorgio Chiellini making frantic appeals for the away fans to behave.
When play resumed Martin Caceres gave the ball away and German Denis pounced from a quick cross, smashing the ball towards goal from inside the box, only to see the base of the post deny him.
Atalanta continued to look dangerous after the restart, but it was Juve which carved out the better opportunities. Emanuele Giaccherini blasted over the bar at the end of a counter, before Matri missed a gilt-edged cross from Isla yards out.
The game exploded back into life in the 81st minute. Federico Peluso avoided a penalty call for a clear handball and Juve was swiftly down the other end of the pitch, with substitute Arturo Vidal seeing a close-range effort denied by Andrea Consigli.
That was the last meaningful action of the match, but Atalanta perhaps was not too disappointed in the final score, as results elsewhere confirmed the club'a survival for another campaign.