Midfielders Marten de Roon and Mario Pasalic scored late as Atalanta beat Udinese 2-0 to surge back into the top four in Serie A on Monday.
The side from Bergamo move ahead of Roma into the final Champions League spot days after booking their ticket to the Coppa Italia final on May 15 against Lazio.
The battle for elite European football next season remains tight with six teams in the running to join Juventus and Napoli in the competition next season.
Atalanta with 59 points from 34 games move one point ahead of Roma who drop to fifth with four games left of the campaign.
"We're experiencing something remarkable, the lads are doing incredible things," said coach Gian Piero Gasperini as his team target a place in top-tier European football for the first time.
"It's in our hands now."
"This is the extraordinary thing about this championship and it makes everything even more fascinating."