Key Moments
The London club's chances of qualifying automatically for the European Cup knockouts were hit hard as their Italian opponents overturned a deficit to win in Bergamo.
Both sides entered this game with identical points tallies in the initial stage of this season's tournament, having secured three victories, tied one, and lost to have accrued 10 points.
For extended periods there was not much to distinguish them in this encounter too, even though Chelsea got their noses in front in the first half when Joao Pedro turned in Reece James' cross.
But Atalanta always looked a threat going forwards, with former Premier League attacker Ademola Lookman issues for the backline.
Reece James shot wide in the second half but Atalanta upped the pressure and deservedly levelled when former West Ham United striker headed in a centering pass.
The winger hammered a powerful shot straight at the keeper but they secured the winning goal in the closing stages when the Blues defence backed off Charles de Ketelaere, who made no mistake with a powerful shot.
The visitors tried to rescue a point in stoppage time but a superb stop by Marco Carnesecchi kept out Pedro.
The result means Chelsea fall out of the automatic qualification places—the spots that qualify automatically for the next round—to 11th with two league phase matches left to play.
Atalanta, meanwhile, climb up to third, three points clear of the Blues.
This was a extremely frustrating result for Chelsea as even a draw was keeping them well placed to achieve the top-eight position they need to avoid the lottery of the play-offs.
But they lost focus in defence with seven minutes remaining and Atalanta capitalised completely.
The Italians are in rich vein of form at the moment so this was always going to be a difficult test for the visitors, but they will be frustrated to be departing with nothing after securing the early advantage.
But the wider issue is that this continues Chelsea's troubling sequence of results in all competitions.
Since beating Barcelona 3-0 at the end of November they are now winless in their last four outings.
Chelsea boss Enzo Maresca made five alterations for this match as he persisted with his strategy of rotating players in and out of the starting lineup.
The changes here followed after he implemented the same number for the loss to Leeds and six for the tie with Bournemouth prior to the trip to Bergamo.
The coach will see rotation as necessary as he tries to manage players' minutes and challenge both at home and abroad, but he insisted the key nucleus of players remains the unchanged for crucial games.
"I believe tonight [in] the first XI we had eight or nine players who played against Tottenham Hotspur, Barcelona, and the Gunners," he commented.
"If you look at the five alterations that we did compared to Bournemouth it may be a change but it is the eight or nine players playing Barcelona.
"The ones who played this evening are the individuals playing almost all the matches."
The Blues' next Champions League game sees them welcome the Cypriot side on the coming Wednesday (8pm GMT).
The Italian team, on the other hand, host Athletic Bilbao at the same time.
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