The legendary trequartista marked his last outing for the Bianconeri with a trademark effort, finding the bottom left corner with a 25-yard shot just before the half-hour
Luca Marrone opened the scoring for the Bianconeri before Alessandro Del Piero brought the house down by marking his final league game for the Old Lady with a 28th-minute strike.
A Stephan Lichtsteiner own goal gave Atalanta late hope of snatching a draw but Andrea Barzagli ensured that Juventus ended their unblemished campaign on a winning note by firing home an injury-time penalty.
Atalanta actually made the brighter start at Juventus Stadium, with German Denis drawing a reaction save out of Marco Storari with a near-post header from a Gianpaolo Bellini cross after just three minutes of play.
However, it was Juve who opened the scoring, Marrone unleashing a fearsome drive which clipped the post on its way past an understandably stationary Giorgio Frezzolini.
It was a blistering strike from the 22-year-old midfielder but much of credit for the goal had to go to Marco Borriello, who had surged into the area before cleverly backheeling the ball into the path of the onrushing Marrone.
The Bianconeri very nearly doubled their advantage on 16 minutes but Simone Padoin unwisely tried to tee up Del Piero after breaking into the area when he really should have gone for goal himself.
The World Cup winner, of course, has never needed any help finding the back of the net and he took the opportunity to underline as much just before the half-hour mark.
Collecting a lay-off from Emanuele Giaccherini some 25 yards out, Del Piero set himself before curling the ball into the bottom left corner of the Atalanta net the poise and precision Juventus fans have become so accustomed to over the past 19 years.
Atalanta really should have pulled a goal back on the half-hour mark but Denis fired horribly over the bar after bursting into the box and past Leonardo Bonucci.
As it was, Juventus reached the interval with their two-goal advantage intact and they thus treated the remainder of the game as nothing more than an exhibition game for their No. 10.
Indeed, events on the field during the second half became a mere sideshow to the extended lap of honour Del Piero undertook shortly after being subbed on 57 minutes.
Atalanta, though, did make a game of it when Lichsteiner diverted a cross from Bellini past his own goalkeeper, but Juventus, fittingly, had the final say, with Barzagli converting from the spot after substitute Fabio Quagliarella had been pulled down in the box by Thomas Manfredini.
The party really began thereafter, as the Serie A trophy was then presented to Juventus, who can now record a double by beating Napoli in the Coppa Italia final in Rome next weekend.