Dusan Vlahovic's fourth-minute strike was enough for Juve to claim the cup for the 15th time in a largely uninspiring final in Rome.
Massimiliano Allegri's side had won just three matches since the end of January coming into the final but frustrated Atalanta from the moment Vlahovic, who also had a goal disallowed for offside in the second half, netted the only goal of the game.
Wednesday's win ended a three-year trophy drought for Juventus, Italy's most successful and widely-supported club.
Atalanta were fancied to win their first major honour since winning the cup in 1963 after a fabulous season for the traditionally provincial club.
However Gian Piero Gasperini's team couldn't find a way through a brilliantly organised Juventus defence which stopped attack-minded Atalanta from having a single shot on target.
The closest Atalanta came to levelling was when Ademola Lookman thumped a shot off the base of the post with 10 minutes remaining.
Atalanta now turn their attentions to sealing Champions League football through Serie A and next week's Europa League final.
The Bergamo club, who are fifth in Italy's top flight, face Bayer Leverkusen in Dublin in their first ever European final.
