Both sides went into this game with identical records in the league phase of this year’s tournament, having won three, drawn one and lost one to sit on 10 points.
For large parts there was little to separate them in this game, too, although Chelsea got their noses in front in the first half when Joao Pedro turned in Reece James’ cross.
But Atalanta always looked a threat going forwards, with former Charlton and Everton attacker Ademola Lookman causing problems.
James shot wide in the second half but Atalanta upped the pressure and deservedly levelled when ex-West Ham striker Gianluca Scamacca headed in a cross.
Alejandro Garnacho drove a strong effort straight at the goalkeeper but Atalanta got the winner late on when the Blues defence backed off Charles de Ketelaere, who took full advantage with a driven strike.
Chelsea tried to rescue a point late on but a superb save by Marco Carnesecchi denied Pedro.
The result means Chelsea drop out of the top eight – the places that qualify automatically for the knockouts – to 11th with two league phase games remaining.
Atalanta, meanwhile, leap up to third, three points ahead of the Blues.
