The Italy midfielder glided between the back line to head his side ahead in the 36th minute and then thumped in a loose ball for his third goal in two games after scoring in Tuesday's 1-0 victory at Maccabi Haifa in the Champions League.
Jaime Valdes pulled one back after the break for the Bergamo side trained by Antonio Conte, a contender for the job in Turin in the close season before his old Juve team mate Ciro Ferrara was promoted from caretaker to permanent coach.
Brazil midfielder Felipe Melo restored the visitors' cushion with a piledriver into the corner from well outside the box.
Atalanta's Fabio Ceravolo exposed the defensive fragility behind Juve's recent inconsistency in Serie A in the 71st, stepping inside his marker before curling the ball inside the far post.
But Diego and David Trezeguet were on target in the closing stages to wrap up a victory that gives them 24 points from 12 games, four points adrift of Inter Milan, who entertain AS Roma on Sunday.
IMPORTANT ACHIEVEMENT
It was Trezeguet's 167th goal for Juventus since he joined them in 2000 to equal the tally notched at the club by 1950s and 60s great Omar Sivori.
"I'm really happy. It's an important achievement," the Frenchman, who was his side's only available striker with Amauri suspended and Alessandro Del Piero and Vincenzo Iaquinta unfit, told Sky television.
"I never thought I'd catch Sivori when I arrived at Juve.
"The important thing is that we played an excellent match and have shown we have desire and are a tough side. Now we have to be consistent."
Earlier Napoli's impressive form under new coach Walter Mazzarri appeared to fizzle out when they were held 0-0 at second-from-bottom Catania.
Napoli, who now share fifth place with Fiorentina, showed none of the fury that had enabled them to come from behind to beat Juventus 3-2 last weekend, their third win in four games after Mazzarri replaced Roberto Donadoni.
The Sicilians were more enterprising and Japanese forward Takayuki Morimoto missed a glorious opportunity before the break when he blasted at the keeper from short range with the goal gaping.
