Manchester United beat CSKA 2-1, finishing top of Group A and progressing alongside second-placed Basel.
United fell behind on the stroke of half-time thanks to Alan Dzagoev's goal.
However, quickfire goals from Romelu Lukaku and Marcus Rashford put the Red Devils ahead with roughly 25 minutes remaining.
Bayern claimed revenge for their drubbing at the hands of PSG earlier in the season, but nevertheless finished second in Group B behind the French giants.
Robert Lewandowski opened the scoring for the Germans in the eighth minute before Corentin Tolisso's header made it 2-0 in the 37th.
Kylian Mbappé pulled a goal back early in the second half, but Tolisso then netted the winner for Bayern in the 69th minute.
Chelsea were knocked off top spot in Group C as a result of their 1-1 draw with Atlético.
Atlético took the lead in the 56th minute through Saul Niguez, with former Chelsea striker Fernando Torres getting the assist. However, 19 minutes later, a Stefan Savic own goal gifted the Blues an equaliser.
Chelsea finished level on points with Roma at the top of the group, but Roma's 3-0 win over Antonio Conte's side saw the Italians finish top by virtue of a superior head-to-head record.
Barcelona knocked Sporting out of the Champions League with a 2-0 win.
Paco Alcácer's header put the Blaugrana ahead in the 59th minute before Jérémy Mathieu's late own goal sealed the game.
Juventus qualified in second place in Group D behind Barcelona, wrapping it up with a 2-0 win over Olympiacos.
Juan Cuadrado scored in the 15th minute to put Juve on the brink of qualification before Federico Bernardeschi sealed the game.
Benfica 0-2 Basel (Qualified)
Celtic 0-1 Anderlecht
(Qualified) Roma 1-0 Qarabag