Antonio Conte's men picked up a narrow victory over the visitors just a day after it was confirmed they had won the Italian top flight once again.
Roma's defeat to Catania on Sunday secured Juve's third consecutive league crown, and the 30th in their history, without Antonio Conte's men even having to play.
In their first game since their latest title was sealed, Padoin netted his first goal for the club to secure a 31st league victory of the season four days after Thursday's Europa League semifinal exit at the hands of Benfica.
After a sluggish opening hour that saw Pablo Osvaldo waste three chances, Juventus was sparked into life by the introduction of Fabio Quagliarella and Carlos Tevez.
The former had two chances soon after coming on at halftime, and his Argentine teammate could have netted with his first touch in the 69th minute, but it fell to Padoin to strike the decisive blow with a well-taken low finish.
One goal was enough for the home fans to raise the volume up another notch as yet another win move Turin giants on to 96 points and well on course to break the 100-point barrier with two games remaining, while the visitors remain 11th.
With the title in the bag Conte rested the majority of his first team regulars and lined up with nine Italian players in his starting lineup, including goalkeeper Marco Storari coming in for Gianluigi Buffon.
Sebastian Giovinco was also given a rare start, and the striker wasted two early chances to put the champions in front.
On both occasions the former Parma man was able to find space on the edge of the penalty area but dragged his shots wide of Andrea Consigli's goal.
Osvaldo sent a long-range effort over the crossbar as the hosts applied pressure, but were unable to find a way through and Atalanta were equally as wasteful on their rare counter attacks.
Claudio Marchisio and Osvaldo had further openings to break the deadlock before the break but were unable to find the back of the net.
Quagliarella was introduced at the break at the expense of the wasteful Giovinco, and he had a chance to spark the party into life in the opening minutes of the second half.
An intricate passing move on the edge of the penalty area found the substitute with a clear sight of goal, but he blasted over the crossbar - much to the frustration of the home support.
After intense pressure from the hosts that saw Tevez and Quagliarella go close, Juve finally found the back of the net through former Atalanta midfielder Padoin in the 72nd minute.
Quagliarella let a pass from the left run across his body, and the 30-year-old fired low into the bottom corner from the edge of the penalty area to seal all three points.