Jose Mourinho's side finished the game with 29% possession and eight shots to Atalanta's 17, but they were far more efficient with their chances.
"Yes, I think so," Mourinho told DAZN when asked if it was the best Roma have played this season. "We showed fantastic spirit. The players knew that we couldn't be in control for 90 minutes against Atalanta. They were strong in every perspective."
Roma moved to 31 points, six behind the Bergamo club in third, and ended a six-game league winning streak by Gian Piero Gasperini's side.
England international Abraham opened the scoring inside the opening minute with a deflected strike, and Nicolo Zaniolo doubled their lead by finishing off a quick counter attack for his first league goal of the season.
Gasperini was quick to make a change, bringing on striker Luis Muriel after 34 minutes, and the Colombian substitute's strike cannoned off Roma's Bryan Cristante for an own goal that got the hosts back into the match on the brink of half time.
Atalanta pushed for a leveller and thought they had it when Jose Luis Palomino nodded in from close range at a corner, but he was offside.
Mourinho's team scored a third four minutes later when Chris Smalling volleyed home his second goal in two games, marking the first time in Serie A history that two different English players have scored in the same game.
Abraham swept in his second of the afternoon with eight minutes remaining to take his tally for the season to six goals in Serie A.