The Blues led at halftime through João Pedro's near-post finish but were stunned after the break as the Serie A side hit back.
First, former West Ham striker Gianluca Scamacca was left unmarked to head the equaliser 10 minutes into the second half, then a fabulous late strike from Charles De Ketelaere, who smashed his finish beyond Robert Sánchez, won it.
"After the goal we conceded we lost control," said Maresca. "Second half, we had two good chances to score the second goal. When we conceded the 1-1, we lost some concentration. We can avoid both of the goals we conceded. They're easy goals."
Chelsea had looked to be on top at the break and were heading towards the win that would have put them on the brink of an automatic place in the last 16.
The impressive Trevoh Chalobah, who had been booked, and Enzo Fernández were then taken off which seemed to disturb the team's rhythm and allow Atalanta back into it.
"Both changes were because Trev and Enzo, they are playing every minute of every game," said Maresca. "They are both not 100 percent. Trev was on a yellow card. This is the reason why we changed them."
Chelsea are like to now need wins in both of their remaining fixtures.
The face Cypriot side Pafos at Stamford Bridge in January before finishing with a difficult trip to face Antonio Conte's Serie A champions Napoli.
Fail to take maximum points and there will almost certainly be a playoff match to contend with in February, further complicating and already crowded schedule.
"We are aware [how crowded their schedule will be with a playoff]," said Maresca. "Absolutely. Now the game is finished. The focus is on Saturday's game [against Everton]. We need to win games.
"Probably we need two wins. Sixteen points might get you top eight, I'm not sure. The next one, for sure, if we want to finish top eight, we need to win both."
The game became open following Pedro's goal and Atalanta took advantage just before the hour mark. The impressive De Ketelaere received the ball in space wide on the right, and as the ball came over, no one in Chelsea white went with Scamacca who rose unmarked in the six-yard box to nod it down and in past Sánchez.
A draw might have been a fair result, then with seven minutes to play, De Ketelaere burst past Marc Cucurella and crashed the winning goal past Sánchez.
"For sure we conceded two goals that for me we can avoid," said Maresca. "When you concede, the first one is the moment when you can't lose the control of the game but I have a feeling that we lost the control of the game after the goal we conceded."
