Rome - Duvan Zapata and Marten de Roon scored second-half goals as Atalanta condemned Roma to a first league defeat of the season on Wednesday, dashing England international defender Chris Smalling's hopes of a winning debut.
The win at the Stadio Olimpico allowed Atalanta to climb into third place in the Serie A table, three points behind leaders and defending champions Juventus ahead of the day's later games.
Paulo Fonseca's Roma, meanwhile, are in fifth spot, five points off the pace.
Atalanta opened the scoring in the 71st minute when Colombian international Zapata, on as a second-half substitute, tucked the ball away from close range.
Dutch midfielder De Roon made sure of the victory with a last-minute, close-range header after Roma goalkeeper Pau Lopez failed to collect a cross.
It was a disappointing night for Smalling as the 31-time capped defender finally made his Roma debut after moving on loan to Italy from Manchester United in the summer.
Later Wednesday, Inter Milan, who have a perfect four wins in four matches, host Lazio where victory will allow them to return to top spot in place of Juventus who defeated Brescia 2-1 on Tuesday.