Key Moments
The London club's ambitions of qualifying automatically for the Champions League knockouts were dealt a blow as Atalanta came from behind to win in Bergamo.
The two teams went into this fixture with matching records in the league phase of this season's tournament, having won, drawn, and suffered one defeat to have accrued ten points.
For much of the game there was very little to distinguish them in this contest too, although Chelsea took the lead in the first half when the Brazilian finished Reece James' delivery.
But Atalanta consistently appeared a threat going on the attack, with ex- Charlton and Everton attacker creating issues for the backline.
Reece James shot wide in the second half but Atalanta raised the pressure and justly drew level when ex-West Ham striker nodded home a centering pass.
Alejandro Garnacho hammered a powerful shot straight at the keeper but they scored the winning goal in the closing stages when the Chelsea defenders retreated from the midfielder, who took full advantage with a low shot.
The visitors tried to salvage a point late on but a excellent save by the Atalanta goalkeeper denied Joao Pedro.
The result means Chelsea slip out of the top eight—the spots that qualify automatically for the knockouts—to eleventh with two league phase games left to play.
The Bergamo club, in contrast, jump up to third, three points clear of the Londoners.
This was a hugely disappointing outcome for Chelsea as even a draw was leaving them well placed to secure the top eight finish they need to avoid the uncertainty of the qualifying play-off round.
But they let their concentration slip in their defensive duties with seven minutes remaining and Atalanta took full advantage.
The Italian side are in fine fettle at the moment so this was always going to be a tough examination for the Blues, but they will be annoyed to be leaving with nothing after taking the lead.
But the bigger picture is that this continues Chelsea's concerning sequence of form in all competitions.
Since defeating the Spanish giants 3-0 at the close of November they are now without a win in their last four outings.
Manager Enzo Maresca enacted five rotations for this game as he continued his strategy of rotating players in and out of the starting lineup.
The rotations here came after he implemented the same number for the defeat to Leeds and six for the tie with Bournemouth prior to the trip to Atalanta.
The coach will see squad rotation as essential as he tries to manage players' fitness and challenge both at domestically and in Europe, but he insisted the core group of players stays the unchanged for important fixtures.
"I believe tonight [in] the starting lineup we had eight or nine players who played against Tottenham, Barcelona, and the Gunners," he commented.
"If you see the five changes that we made compared to Bournemouth it is different but it is the same eight or nine players who played in that match.
"The ones who took to the field tonight are the ones playing almost all the games."
The Blues' next Champions League game sees them host Pafos on the coming Wednesday (20:00 GMT).
The Italian team, on the other hand, are at home to Athletic Club at the same time.
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