The Giallorossi went behind early on thanks to goals from Andreas Cornelius and Marten De Roon - before the latter man was sent off moments before half-time.
Eusebio Di Francesco's side came out in determined fashion in the second half, and soon halved the deficit through Edin Dzeko.
But an equaliser would not be forthcoming, as the team's poor recent run continued.
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The result means the Giallorossi drop to fifth as Serie A moves into the winter break.
With Daniele De Rossi injured and Radja Nainggolan left out for disciplinary reasons, Roma started with Maxime Gonalons, Lorenzo Pellegrini and Kevin Strootman in midfield.
In attack, Stephan El Shaarawy returned to the starting line-up, alongside Edin Dzeko and Diego Perotti.
5' - Pellegrini takes a touch and hits an early shot that Berisha saves comfortably.
12' - El Shaarawy hits the first-time half-volley from the edge of the box, forcing Berisha into a good save low to his right.
14' - Goal. Atalanta lead. Cornelius cuts onto his left-foot and finds the bottom corner. 0-1.
19' - Goal. Atalanta double their lead. De Roon's shot takes a deflection and finds the far corner. 0-2.
28' - De Roon is booked for a foul on Perotti.
31' - Kolarov's free-kick takes a deflection off Dzeko but, with Berisha completely beaten, the ball flies inches wide of the post.
37' - Freuler's low first-time hit from a half-cleared corner bounces off the post, Alisson and away.
42' - Dzeko takes the defender on, cuts onto his right foot, and curls a low shot just inches wide of the far post!
45' - RED CARD! Kolarov beats Ilicic, then tries to go past Marten De Roon but is brought down. The midfielder has already been booked, so he's off!
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48' - Gomez forces a good save from Alisson. From the corner, Caldara heads narrowly over.
54' - CLOSE! Dzeko's powerfully meets Perotti's cross, but the ball deflects off a defender and Berisha is able to turn and hold onto it!
56' - GOAL! ONE BACK! El Shaarawy plays in Dzeko who runs onto the ball inside the box and then fires low across Berisha for a crucial goal. 1-2!
61' - CLOSE! Kolarov fires fractionally wide from 30 yards!
70' - Florenzi crosses for Dzeko, but the striker cannot put his header on target.
85' - How did that not go in?! Peres crosses for El Shaarawy, but his first header is blocked and then his follow-up shot is somehow blocked by Masiello!
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“In the first half it was shameful to play like that at our stadium. I think it’s a mental thing, perhaps we lack a bit of confidence. I really don’t think it’s a physical or tactical problem.“In the first half it felt like we were playing 11 against 13 or 14, because we were always getting to the ball second. We need to get past this difficult moment and work hard to get back to our usual level."
- Kevin Strootman
“We’ve taken a few steps back, for sure. Now we must all apologise and realise that in order to be clinical we have to come together as a team. We’ll have a chance to do that during the winter break. We have to recharge our batteries physically and mentally, we need to reset and start again to be the team that we were before this period. We cannot play like this.”
- Eusebio Di Francesco
Serie A now takes a short winter break - the Giallorossi are next in action on Sunday January 21, as they face Inter Milan at San Siro.
Goalscorers: (Dzeko (56'); Cornelius (14'), De Roon (19')
Red cards: De Roon (45')
Roma: Alisson; Florenzi (Peres), Manolas, Fazio, Kolarov; Gonalons, Strootman (Cengiz), Pellegrini (Schick); Perotti, Dzeko, El Shaarawy,
Atalanta: Berisha; Toloi, Caldara, Palomino; Hateboer, de Roon, Freuler, Spinazzola; Iličić, Cornelius, Gomez
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