Match Summary
The London club's hopes of qualifying automatically for the Champions League knockout stages were hit hard as Atalanta fought back to triumph in their home stadium.
Both sides entered this match with identical records in the league phase of this season's competition, having won, drawn, and suffered one defeat to be on 10 points.
For extended periods there was not much to choose between them in this encounter too, even though Chelsea took the lead in the opening 45 minutes when Joao Pedro finished the captain's delivery.
But Atalanta always looked a threat going on the attack, with former Charlton and Everton attacker Ademola Lookman problems for the backline.
James fired wide in the after the break but the home team raised the intensity and justly levelled when former West Ham United striker nodded home a cross.
Alejandro Garnacho drove a strong effort straight at the goalkeeper but they got the decisive strike in the closing stages when the Blues defence retreated from Charles de Ketelaere, who made no mistake with a driven shot.
The visitors tried to rescue a draw in stoppage time but a superb stop by Marco Carnesecchi kept out Joao Pedro.
The result means Chelsea drop out of the top eight—the spots that progress automatically for the next round—to eleventh with two group stage games remaining.
Atalanta, meanwhile, leap up to third, three points ahead of the Londoners.
This was a deeply disappointing outcome for Chelsea as even a point was leaving them in a strong position to secure the top-eight position they require to avoid the uncertainty of the qualifying play-off round.
But they lost focus in defence with seven minutes remaining and their opponents seized the moment.
The Italian side are in fine fettle at the moment so this was always going to be a challenging examination for the visitors, but they will be annoyed to be departing with no points after taking the early advantage.
But the wider issue is that this continues Chelsea's concerning sequence of results in all tournaments.
Since beating Barcelona 3-0 at the end of November they are now without a win in their last four matches.
Chelsea boss Maresca made five alterations for this game as he persisted with his strategy of rotating players in and out of the starting lineup.
The changes here came after he made the identical amount for the loss to Leeds and six for the draw with Bournemouth prior to the journey to Atalanta.
Maresca will view rotation as vital as he attempts to manage players' fitness and challenge both at domestically and in Europe, but he maintained the core group of players remains the unchanged for important games.
"I think tonight [in] the starting lineup we had eight or nine players who played against Tottenham, FC Barcelona, and Arsenal," he said.
"If you see the five alterations that we did compared to Bournemouth it is different but it involves the eight or nine players who played Barcelona.
"The players who took to the field this evening are the individuals who feature in almost all the matches."
The Blues' next European game sees them host Pafos on the coming Wednesday (8pm GMT).
The Italian team, on the other hand, host Athletic Club at the same time.