Key Moments
The London club's hopes of securing a place automatically for the Champions League knockouts were dealt a blow as their Italian opponents overturned a deficit to triumph in Bergamo.
Each club went into this game with identical points tallies in the league phase of this season's competition, having won, tied one, and suffered one defeat to be on 10 points.
For extended periods there was little to choose between them in this encounter too, although Chelsea took the lead in the first half when Joao Pedro finished the captain's delivery.
But Atalanta remained a danger going on the attack, with former Premier League attacker causing issues for the defence.
Reece James fired wide in the after the break but Atalanta increased the pressure and justly levelled when former West Ham United striker headed in a cross.
The winger drove a powerful shot straight at the goalkeeper but Atalanta got the winning goal in the closing stages when the Chelsea defence backed off the midfielder, who made no mistake with a driven finish.
The visitors tried to rescue a point late on but a brilliant stop by Marco Carnesecchi kept out Pedro.
The final score means Chelsea fall out of the top eight—the spots that progress automatically for the next round—to eleventh with two league phase matches left to play.
Atalanta, meanwhile, climb up to third place, three points clear of the Londoners.
This was a hugely disappointing outcome for Chelsea as even a point was leaving them well placed to secure the top eight position they require to bypass the lottery of the qualifying play-off round.
But they lost focus in their defensive duties with seven minutes remaining and Atalanta took full advantage.
The Italians are in rich vein of form at the moment so this was always going to be a difficult examination for the visitors, but they will be frustrated to be departing with nothing after securing the lead.
But the wider issue is that this extends Chelsea's concerning run of form in all tournaments.
Since beating the Spanish giants 3-0 at the end of November they are now winless in their last four games.
Chelsea boss Enzo Maresca made five changes for this match as he persisted with his run of moving players in and out of the first team.
The changes here followed after he implemented the same number for the loss to Leeds United and six for the draw with AFC Bournemouth prior to the journey to Atalanta.
Maresca will see rotation as vital as he tries to handle players' fitness and compete both at domestically and in Europe, but he stated the key nucleus of players remains the unchanged for key games.
"I think tonight [in] the first XI we had eight or nine players who played against Tottenham, Barcelona, and the Gunners," he said.
"If you look at the five changes that we did relative to the previous game it is a change but it involves the eight or nine players playing Barcelona.
"The ones who took to the field tonight are the ones who feature in almost all the matches."
The Blues' next Champions League fixture sees them welcome Pafos on the coming Wednesday (8pm GMT).
The Italian team, on the other hand, are at home to Athletic Club at the identical kick-off time.
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