Match Summary
The London club's chances of securing a place automatically for the European Cup knockouts were suffered a setback as their Italian opponents fought back to triumph in their home stadium.
The two teams went into this game with matching records in the initial stage of this year's competition, having won, tied one, and suffered one defeat to be on 10 points.
For extended periods there was very little to choose between them in this encounter too, even though Chelsea took the lead in the first half when Joao Pedro finished the captain's cross.
But The Serie A side remained a threat going forward, with ex- Charlton and Everton attacker causing problems for the backline.
Reece James fired wide in the after the break but the home team increased the intensity and justly drew level when ex-West Ham striker nodded home a cross.
The winger hammered a powerful shot straight at the goalkeeper but Atalanta secured the winning goal in the closing stages when the Blues defence retreated from Charles de Ketelaere, who seized the opportunity with a powerful strike.
The visitors attempted to rescue a draw in stoppage time but a excellent stop by Marco Carnesecchi denied Pedro.
The result means Chelsea slip out of the top eight—the spots that qualify automatically for the next round—to eleventh with two group stage matches remaining.
Atalanta, meanwhile, jump up to third place, three points clear of the Blues.
This was a hugely frustrating result for Chelsea as even a draw was keeping them well placed to secure the top-eight finish they need to bypass the uncertainty of the play-offs.
But they let their concentration slip in their defensive duties with seven minutes remaining and Atalanta seized the moment.
The Italians are in fine fettle at the moment so this was always going to be a challenging examination for the visitors, but they will be frustrated to be leaving with nothing after taking the lead.
But the bigger picture is that this perpetuates Chelsea's troubling sequence of form in all tournaments.
Since beating Barcelona 3-0 at the close of November they are now without a win in their last four outings.
Chelsea boss Enzo Maresca enacted five changes for this game as he persisted with his policy of moving players in and out of the first team.
The changes here came after he made the same number for the defeat to Leeds and six for the tie with Bournemouth prior to the trip to Bergamo.
Maresca will view squad rotation as necessary as he attempts to handle players' minutes and compete both at home and in Europe, but he stated the key nucleus of players stays the same for important fixtures.
"I think tonight [in] the first XI we had eight or nine players who featured against Tottenham, Barcelona, and Arsenal," he commented.
"If you see the five changes that we did relative to Bournemouth it may be different but it is the eight or nine players who played in that match.
"The players who played tonight are the ones playing almost all the matches."
Chelsea's next Champions League game sees them welcome Pafos on the coming Wednesday (20:00 GMT).
Atalanta, on the other hand, are at home to Athletic Club at the identical kick-off time.
Mira is a tech journalist and AI researcher with over a decade of experience covering emerging technologies and their societal impacts.