Leverkusen fell to third place in Group A, one point behind Shakhtar Donetsk which beat Real Sociedad 4-0 thanks to goals from Adriano, Alex Teixeira and Douglas Costa, who netted twice.
Shakhtar faces United at Old Trafford in the final round of group games, with Leverkusen away to winless Sociedad.
Bayern Munich became the first team to win 10 consecutive Champions League games as the holder again showed its determination to retain the trophy.
Pep Guardiola's German giant was a 3-1 winner over CSKA Moscow in the icy cold Russian capital thanks to goals from Arjen Robben, Mario Gotze and Thomas Muller.
Muller converted a 65th-minute penalty to seal the win, three minutes after Keisuke Honda had given CSKA brief hope.
Bayern will advance from Group D alongside Manchester City which toiled for a 4-2 win at home against Viktoria Plzen, a team which almost pinched a first point of the campaign.
Sergio Aguero and Samir Nasri twice put City ahead, but Tomas Horava dragged Plzen back in it at half-time and Stanislav Tecl left all to play for at 2-2 when he struck low beyond Joe Hart in the 69th minute.
Alvaro Negredo, another expensive foreign import by the 2012 Premier League champion, gave Manuel Pellegrini's side the lead again with a 78th-minute winner, and Edin Dzeko headed a late fourth.
Midfielder Arturo Vidal scored a hat-trick to steer Juventus to a 3-1 home win over FC Copenhagen that lifted the Italian side from bottom place in Group B up to second.
Vidal scored two penalties, sandwiching an equaliser from Olof Mellberg, and sealed his treble in the 63rd minute by heading in Paul Pogba's cross.
Real Madrid secured first place in Group B with a 4-1 win over Galatasaray, despite losing Sergio Ramos to an early red card.
Defender Ramos was dismissed in the 26th minute, and 11 minutes later Gareth Bale gave Madrid the lead with a fine free-kick, only for the advantage to be almost instantly wiped out by Umut Bulut.
Alvaro Arbeloa and Angel di Maria netted in the first 20 minutes of the second half, and Isco added a fourth goal for the host late on.
Benfica improved its prospects of joining Paris Saint-Germain in qualifying from Group C after beating Anderlecht 3-2 in Brussels.
Chancel Mbemba and Massimo Bruno scored for Anderlecht, but Nemanja Matic, an Mbemba own goal, and Moreno Rodrigo's 90th-minute low finish earned three points for the Portuguese visitor.
Benfica moved level on points with Olympiacos in the battle for second place, after the Greek side lost 2-1 in Paris.
Zlatan Ibrahimovic put Paris Saint-Germain ahead after just seven minutes, but the French side was down to 10 men early in the second half when Marco Verratti was sent off for a second yellow-card offence.
Kostas Manolas snatched an equaliser with 10 minutes remaining, but Edinson Cavani poked in a late winner for the Ligue 1 champion.