Luis Enrique's side turned in a poor display to put its Champions League hopes in danger ahead of the match between Napoli and Inter at the San Paolo late this evening
The hosts started out the brighter and almost took the lead just two minutes in. Guido Marilungo received a long ball on the edge of the box and moved past Juan, but his shot hit the right post of Maarten Stekelenburg's goal.
But just six minutes later, Marilungo was more incisive and opened the scoring, calmly sending the ball past Stekelenburg after being played through by German Denis.
Atalanta doubled its lead in the 19th minute as it hit Roma on the break. Denis played a one-two with Maxi Moralez before firing home a low finish.
Roma at this stage knew it had a mountain to climb, but reduced the deficit in the 36th minute. Rodrigo Taddei cut the ball back from the left and Fabio Borini slotted home from close range after Pablo Osvaldo's first attempt had been deflected.
It was expected that the Giallorossi would stay on the same path after the break, but Atalanta came out strongly in the second half and restored a two-goal lead in the 47th minute, when Denis tapped home a low Marilungo cross from the right.
Things went from bad to worse for Roma shortly after, as Osvaldo was sent off for kicking out at Luca Cigarini from behind.
Atalanta piled more misery on the visitors in the 66th minute, when Denis completed his hat trick as he sent the ball over the onrushing Stekelenburg.
In the last minutes of the match, Roma lost its head as it was reduced to nine men after Marco Cassetti was shown red for dissent, to compound an afternoon to forget for Luis Enrique's side.
Follow GOAL.COM USA on