Key Moments
The London club's ambitions of qualifying automatically for the Champions League knockout stages were dealt a blow as Atalanta overturned a deficit to triumph in Bergamo.
Both sides entered this game with identical records in the league phase of this season's tournament, having won, drawn, and suffered one defeat to be on ten points.
For much of the game there was very little to separate them in this encounter too, although Chelsea took the lead in the opening 45 minutes when the Brazilian turned in the captain's delivery.
But The Serie A side consistently appeared a threat going forward, with former Premier League attacker causing problems for the defence.
Reece James fired wide in the after the break but Atalanta upped the pressure and justly equalised when former West Ham United striker headed in a centering pass.
Alejandro Garnacho hammered a strong effort straight at the keeper but they scored the winning goal in the closing stages when the Chelsea defence backed off Charles de Ketelaere, who seized the opportunity with a powerful strike.
Chelsea tried to salvage a draw in stoppage time but a excellent save by the Atalanta goalkeeper denied Pedro.
The outcome means Chelsea slip out of the top eight—the spots that progress automatically for the knockouts—to eleventh with two league phase matches remaining.
The Bergamo club, meanwhile, leap up to third, three points clear of the Blues.
This was a hugely disappointing outcome for Chelsea as even a point was keeping them in a strong position to achieve the top eight finish they require 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 their opponents seized the moment.
The Italians are in fine fettle at the moment so this was always going to be a challenging examination for the Blues, but they will be disappointed to be leaving with no points after taking the early advantage.
But the broader context is that this continues Chelsea's troubling run of form in all competitions.
Since defeating the Spanish giants 3-0 at the close of November they are now winless in their last four matches.
Manager Enzo Maresca enacted five alterations for this match as he continued his policy of rotating players in and out of the first team.
The changes here followed after he made the same number for the defeat to Leeds and six for the tie with AFC Bournemouth prior to the journey to Atalanta.
The coach will see squad rotation as necessary as he tries to handle players' workloads and compete both at domestically and abroad, but he maintained the core group of players stays the same for crucial games.
"I believe in this match [in] the starting lineup we had eight or nine players who featured against Tottenham Hotspur, Barcelona, and Arsenal," he stated.
"If you see the five alterations that we did compared to the previous game it may be a change but it involves the eight or nine players who played Barcelona.
"The players who took to the field tonight are the ones playing almost all the matches."
Chelsea's next European game sees them host the Cypriot side on the coming Wednesday (8pm GMT).
The Italian team, meanwhile, host Athletic Bilbao at the same time.