At a Glance
The London club's ambitions of qualifying automatically for the European Cup knockouts were hit hard as Atalanta fought back to win in Bergamo.
Each club entered this match with the same records in the league phase of this season's competition, having won, drawn, and suffered one defeat to sit on ten points.
For extended periods there was not much to distinguish them in this encounter too, even though Chelsea took the lead in the first half when Joao Pedro converted the captain's cross.
But The Serie A side always looked a danger going forwards, with former Charlton and Everton attacker causing issues for the defence.
Reece James fired wide in the second half but Atalanta raised the pressure and justly drew level when former West Ham United striker Gianluca Scamacca a cross.
Alejandro Garnacho hammered a powerful shot straight at the keeper but they scored the winning goal late on when the Blues defenders backed off the midfielder, who made no mistake with a driven shot.
The visitors tried to rescue a draw late on but a superb save by Marco Carnesecchi kept out Joao Pedro.
The result means Chelsea fall out of the automatic qualification places—the positions that qualify automatically for the knockouts—to 11th with two group stage fixtures remaining.
Atalanta, in contrast, climb up to third, 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 finish they require to avoid the uncertainty of the qualifying play-off round.
But they lost focus in their defensive duties with seven minutes remaining and their opponents seized the moment.
The Italians are in fine fettle at the moment so this was always going to be a tough examination for the visitors, but they will be annoyed to be departing with nothing after taking the lead.
But the wider issue is that this continues Chelsea's troubling streak of form in all competitions.
Since beating the Spanish giants 3-0 at the end of November they are now without a win in their last four matches.
Manager Enzo Enzo Maresca made five changes for this game as he continued his strategy of rotating players in and out of the starting lineup.
The rotations here followed after he made the identical amount for the defeat to Leeds United and six for the tie with Bournemouth prior to the trip to Bergamo.
The coach will view squad rotation as vital as he tries to manage players' fitness and compete both at home and in Europe, but he maintained the core group of players stays the same for important games.
"I think tonight [in] the first XI we had eight or nine players who featured against Tottenham, Barcelona, and the Gunners," he said.
"If you see the five alterations that we did relative to the previous game it is different but it is the eight or nine players playing Barcelona.
"The players who played this evening are the ones who feature in almost all the matches."
The Blues' next European game sees them host the Cypriot side on the coming Wednesday (20:00 GMT).
Atalanta, meanwhile, are at home to Athletic Bilbao at the same time.