Key Moments
The London club's chances of securing a place automatically for the European Cup knockout stages were dealt a blow as Atalanta came from behind to claim victory in their home stadium.
Each club went into this match with matching records in the league phase of this year's competition, having won, drawn, and lost to sit on 10 points.
For extended periods there was not much to separate them in this contest too, even though Chelsea got their noses in front in the first half when the Brazilian turned in Reece James' cross.
But Atalanta consistently appeared a threat going forwards, with ex- Charlton and Everton attacker Ademola Lookman issues for the backline.
Reece James fired wide in the after the break but Atalanta upped the intensity and deservedly drew level when ex-West Ham striker Gianluca Scamacca a cross.
Alejandro Garnacho hammered a powerful shot straight at the goalkeeper but Atalanta got the decisive strike late on when the Blues defenders backed off the midfielder, who seized the opportunity with a low shot.
Chelsea attempted to salvage a draw in stoppage time but a excellent stop by the Atalanta goalkeeper kept out Joao Pedro.
The final score means Chelsea drop out of the automatic qualification places—the spots that progress automatically for the knockouts—to eleventh with two league phase matches remaining.
Atalanta, in contrast, jump up to third, three points ahead of the Blues.
This was a extremely disappointing result for Chelsea as even a draw was keeping them in a strong position to secure the top-eight position they need to avoid the lottery of the qualifying play-off round.
But they lacked concentration in defence with seven minutes left on the clock and Atalanta capitalised completely.
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 leaving with nothing after taking the early advantage.
But the broader context is that this continues Chelsea's worrying run of form in all tournaments.
Since defeating Barcelona 3-0 at the end of November they are now without a win in their last four games.
Manager Enzo Enzo Maresca enacted five changes for this match as he persisted with his policy of rotating players in and out of the starting 11.
The changes here followed after he made the identical amount for the loss to Leeds United and six for the tie with AFC Bournemouth prior to the journey to Bergamo.
Maresca will view squad rotation as necessary as he tries to handle players' fitness and compete both at home and abroad, but he insisted the central contingent of players remains the same for crucial fixtures.
"I think in this match [in] the first XI we had eight or nine players who played against Tottenham Hotspur, Barcelona, and the Gunners," he stated.
"If you look at the five changes that we made compared to the previous game it may be different but it is the eight or nine players playing Barcelona.
"The ones who played this evening are the ones who feature in almost all the matches."
Chelsea's next Champions League fixture sees them host Pafos on Wednesday, 21 January (20:00 GMT).
The Italian team, on the other hand, host Athletic Bilbao at the same time.
Lena is a passionate gamer and tech writer, specializing in indie games and hardware reviews, with years of industry experience.