The Catalan giants were the only club in Europe allowed to sign their former player but, despite holding an interest, were unable to move due to Financial Fair Play (FFP) concerns.
Graham Potter has left the club’s summer signing out of the 25-man Champions League squad, while the former Arsenal forward was not involved during Friday’s Premier League game with Fulham.
The omission from Chelsea’s squad submitted to UEFA on Thursday leaves Aubameyang’s future in serious doubt.
There will be disappointment that he can’t face his former club Borussia Dortmund in the last 16 tie beginning this month.
Third-choice goalkeeper Marcus Bettinelli, 19-year-old midfielder Carney Chukwuemeka and Hakim Ziyech, who saw a loan deal to PSG collapse on deadline day, are among those selected ahead of the Gabon international.
At this stage, there has been no suggestion of any reason for the decision beyond his performances having dipped in recent weeks, which has been true of the team as a whole.
Potter has been largely positive about his striker, refusing to blame him for his lack of goals in recent weeks and Aubameyang remains a popular figure in the dressing room.
Chelsea also left out new signings Benoit Badiashile, David Datro Fofana, Noni Madueke and Andrey Santos -- with only three new signings in Mykhailo Mudryk, Enzo Fernandez and Joao Felix allowed to be made available for the rest of the European campaign.
The Blues have a 33-man squad going into the second half of the season after signing seven players in the January transfer window and selling only Jorginho to Arsenal.