Goals in either half from Dejan Kulusevski and Federico Chiesa gave coach Andrea Pirlo his second second trophy of the season after the Italian Super Cup, on the day he turned 42.
Atalanta coach Gian Piero Gasperini was denied a first trophy of his coaching career, and Atalanta's second trophy after the 1963 Coppa Italia.
It was a boost for Juventus who go into the final weekend of the season with their Champions League qualification going down to the wire after Inter Milan ended their nine-year league reign.
Gianluigi Buffon was in the Juventus goal for the final time in his career and the veteran keeper was solid on the night winning his sixth Coppa Italia 22 years after his first with Parma.