Key Moments
The London club's ambitions of qualifying automatically for the Champions League knockouts were hit hard as Atalanta came from behind to win in their home stadium.
Both sides went into this match with the same points tallies in the league phase of this season's tournament, having won, tied one, and suffered one defeat to be on 10 points.
For extended periods there was not much to choose between them in this contest too, even though Chelsea got their noses in front in the first half when Joao Pedro converted Reece James' cross.
But The Serie A side remained a threat going on the attack, with former Premier League attacker creating problems for the backline.
Reece James shot wide in the second half but Atalanta increased the pressure and deservedly drew level when ex-West Ham striker Gianluca Scamacca a centering pass.
The winger hammered a strong effort straight at the keeper but they got the decisive strike late on when the Chelsea defence backed off the midfielder, who seized the opportunity with a driven strike.
The visitors tried to rescue a point in stoppage time but a brilliant stop by Marco Carnesecchi kept out Joao Pedro.
The final score means Chelsea fall out of the top eight—the positions that progress automatically for the knockouts—to eleventh with two league phase fixtures left to play.
Atalanta, meanwhile, leap up to third place, three points ahead of the Londoners.
This was a hugely frustrating outcome for Chelsea as even a draw was leaving them in a strong position to secure the top eight position they need to bypass the lottery of the qualifying play-off round.
But they lost focus in their defensive duties with seven minutes left on the clock and their opponents capitalised completely.
The Italian side are in good form at the moment so this was always going to be a difficult test for the visitors, but they will be annoyed to be departing with no points after taking the early advantage.
But the bigger picture is that this extends Chelsea's concerning streak of form in all tournaments.
Since beating Barcelona 3-0 at the close of November they are now without a win in their last four matches.
Manager Enzo Maresca made five changes for this match as he continued his policy of moving players in and out of the starting 11.
The changes here followed after he implemented the same number for the defeat to Leeds and six for the tie with AFC Bournemouth prior to the journey to Bergamo.
The coach will see squad rotation as vital as he tries to manage players' fitness and challenge both at domestically and in Europe, but he insisted the central contingent of players stays the unchanged for crucial fixtures.
"I believe in this match [in] the starting lineup we had eight or nine players who featured against Tottenham, FC Barcelona, and Arsenal," he stated.
"If you look at the five alterations that we made compared to Bournemouth 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 playing almost all the games."
The Blues' next Champions League fixture sees them host the Cypriot side on the coming Wednesday (8pm GMT).
Atalanta, on the other hand, host Athletic Bilbao at the same time.