Ibrahim Sulemana’s strike in the 76th minute moved Atalanta, in third, seven points ahead of fifth-placed Lazio with two matches remaining in the season.
Gian Piero Gasperini’s team had taken an early lead through Ademola Lookman only for Atalanta old boy Bryan Cristante to head Roma level in the 32nd minute.
But Sulemana ended Roma’s long unbeaten run at 19 matches and left Claudio Ranieri’s side one point behind Lazio and Juventus, who sit fourth.
Roma can still snatch a spot in Europe’s top club competition but host in-form AC Milan next weekend while Juve welcome Udinese.
Reaching the Champions League would be a huge triumph for Ranieri as Roma looked like relegation candidates when he came out of retirement in November to take charge of his boyhood club for the third time.
Gasperini has been tipped to take over Ranieri after nine hugely successful years in the Atalanta dugout, winning the Europa League last season. (AFP)
