Lazio found two late goals to win the Coppa Italia final and deny Atalanta their first trophy since 1963.
On a filthy wet night in Rome both sides struggled to find any fluent football, although Atalanta twice hit the post.
Midfielder Sergej Milinkovic-Savic came off the bench to head in the opener before forward Joaquin Correa ran clear to wrap it up in stoppage-time.
Lazio will now play in next season’s Europa League.
Fourth-placed Atalanta can still secure Champions League football for the first time if they win their last two games – against Juventus and Sassuolo.
But their chance of silverware is gone for another year as Lazio edged an ill-tempered game littered with bookings.
Former Liverpool midfielder Lucas would have been an unlikely scorer but headed wide for Lazio before former Middlesbrough midfielder Marten de Roon rattled the post for Atalanta.
Papu Gomez hit the post with a miscued cross as Atalanta continued to look the better side, before sub Milinkovic-Savic scored with Lazio’s first effort on target when he headed in Lucas’ corner.
Then, as Atalanta threw men forward Lazio broke and Correa did well to dance around goalkeeper Pierluigi Gollini and score.
Seven-time winners Lazio last won the cup in 2013.