Aubameyang was excluded alongside Benoit Badiashile, who joined the Blues on a £35m deal last month, in the newly released list on Friday.
Chelsea were only allowed to register a maximum of three new players for the knockout stages as they face Borussia Dortmund in the last 16.
Clubs had until 11pm on Thursday, February 2, to inform UEFA of their desired squad changes.
All clubs are limited to a 25-man squad and Chelsea used 24 players in the group stage, with only one of them, Jorginho, leaving the club in the January transfer window.
The three new registered players are allowed to have played for another club in European competitions this season.
Chelsea made eight signings in January for a combined total of £323.3m. Malo Gusto is staying on loan at Lyon and Andrey Santos is waiting for a work permit so that left Graham Potter with the dilemma of picking three players from Fernandez, Mudryk, Felix, Badiashile, David Datro Fofana and Noni Madueke.
Aubameyang is however still included in Chelsea’s 25-man Premier League squad along with their new signings as there are no restrictions on how many changes clubs can make in the EPL
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