Key Moments
The London club's hopes of qualifying automatically for the European Cup knockout stages were hit hard as Atalanta came from behind to win in their home stadium.
Both sides went into this fixture with matching points tallies in the league phase of this season's competition, having secured three victories, tied one, and lost to sit on ten points.
For large parts there was not much to choose between them in this encounter too, although Chelsea took the lead in the opening 45 minutes when Joao Pedro converted the captain's delivery.
But The Serie A side consistently appeared a threat going on the attack, with former Premier League attacker Ademola Lookman issues for the defence.
James shot wide in the second half but Atalanta upped the pressure and justly drew level when former West Ham United striker headed in a centering pass.
Alejandro Garnacho hammered a strong effort straight at the goalkeeper but they secured the winning goal in the closing stages when the Chelsea defenders backed off the midfielder, who seized the opportunity with a low finish.
The visitors tried to rescue a point in stoppage time but a excellent stop by Marco Carnesecchi denied Pedro.
The result means Chelsea fall out of the automatic qualification places—the positions that progress automatically for the next round—to 11th with two league phase matches remaining.
The Bergamo club, meanwhile, leap up to third, three points clear of the Londoners.
This was a hugely disappointing result for Chelsea as even a draw was leaving them in a strong position to achieve the top-eight position they need to avoid the lottery of the qualifying play-off round.
But they lost focus in defence with seven minutes remaining and Atalanta took full advantage.
The Italians are in good form at the moment so this was always going to be a challenging test for the visitors, but they will be annoyed to be leaving with nothing after taking the early advantage.
But the bigger picture is that this continues Chelsea's worrying sequence of form in all tournaments.
Since beating the Spanish giants 3-0 at the close of November they are now winless in their last four outings.
Chelsea boss Maresca made five rotations for this match as he persisted with his run of rotating players in and out of the starting 11.
The changes here followed after he implemented the identical amount for the defeat to Leeds and six for the tie with AFC Bournemouth prior to the journey to Atalanta.
Maresca will view squad rotation as necessary as he attempts to manage players' workloads and challenge both at domestically and in Europe, but he insisted the key nucleus of players remains the unchanged for key games.
"I think in this match [in] the first XI we had eight or nine players who played against Tottenham Hotspur, FC Barcelona, and the Gunners," he commented.
"If you look at the five changes that we did compared to Bournemouth it is a change but it is the eight or nine players playing in that match.
"The ones who played this evening are the individuals who feature in almost all the games."
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 Bilbao at the identical kick-off time.
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