Chelsea took the lead through Joao Pedro in the 25th minute after VAR confirmed Reece James was onside in the build-up.
Atalanta caused Chelsea consistent problems, however, and finally got their equaliser thanks to a simple Gianluca Scamacca header just before the hour mark.
The Serie A side continued to pile on the pressure as Chelsea struggled to create much of a threat before Charles De Ketelaere scored the winner via a big deflection from Marc Cucurella.
Chelsea now have just one win in their last five games across all competitions and have fallen down to 11th in the Champions League league phase.
Speaking after the game, Maresca admitted he’s “worried” about his side’s recent dip in form but insists they controlled the game in the first half.
"First half we were controlling the game,” he told UEFA.
"After the goal we conceded first one we lost a bit of the control of the game. We are playing every two days and we probably look like we struggle a bit.
"We just want to win as soon as possible. We tried to be aggressive, when we conceded 1-1 probably the dynamic of the game changed a bit."
On Chelsea's dip in form: "I am always worried. Two points in four games is not what we expect and we have to do better."