Gabon forward Aubameyang, 33, started all the Blues’ six group matches, scoring two goals.
However, he has since fallen out of favour and was last named in Graham Potter’s starting XI on 6 November.
France defender Benoit Badiashile, a £35m January signing, also misses out.
England Under-21s winger Noni Madueke, a recent £30.7m acquisition from PSV Eindhoven and fellow new arrivals Andrey Santos and David Datro Fofana were also excluded.
However, Morocco winger Hakim Ziyech, whose proposed loan move to Paris St-Germain fell through, does retain a place in Potter’s squad, with clubs only permitted to register a maximum of three new players for the remaining matches in this term’s competition.
Chelsea outlaid a British record 121m euro (£107m) transfer fee to secure the services of Argentine World Cup winner Fernandez from Benfica.
Mudryk’s arrival at Stamford Bridge from Shakhtar Donetsk in a deal worth up to £89m came shortly after the club signed Portugal forward Felix on a loan deal from Atletico Madrid.
Chelsea travel to German club Borussia Dortmund in the first leg of their last-16 tie on Wednesday, 15 February.
Cody Gakpo, Naby Keita and Alex Oxlade-Chamberlain have all been added to Liverpool’s group, with Jurgen Klopp’s side due to play Real Madrid in a repeat of last season’s final, with the first of their two legs at Anfield on Tuesday, 21 February (20:00 GMT).
Argentine midfielder Maximo Perrone has been included in Manchester City’s squad for their matches against RB Leipzig, replacing Portugal full-back Joao Cancelo, who is named in Bayern Munich’s contingent after heading there on loan.
Tottenham have included loan signings Arnaut Danjuma and Pedro Porro in their squad, although Zlatan Ibrahimovic has been omitted by AC Milan, who face Spurs the last 16, with the first leg taking place at the San Siro on 14 February (20:00).
Ibrahimovic, 41, is yet to feature for the Italian champions this season after having knee surgery last summer having helped the club to its first Scudetto for 11 years.
Source: BBC