Juande Ramos began his reign as Real Madrid coach with a 3-0 home win over Zenit St Petersburg in the Champions League on Wednesday while Dynamo Kiev and Fiorentina booked UEFA Cup berths.
Holders Manchester United took top spot in Group E despite being held 2-2 at home by Danes AaB Aalborg. Villarreal were second after a 2-0 defeat at Celtic.
Two goals from Raul and a third by Arjen Robben gave Real victory over UEFA Cup holders Zenit in their first match under Ramos, who replaced the sacked Bernd Schuster on Tuesday.
The nine-times European champions finished second on goal difference in Group H behind Juventus, who were held 0-0 at home by BATE Borisov.
A Roman Eremenko goal gave Dynamo a 1-0 win over Fenerbahce to earn a spot in the UEFA Cup as third-place finishers in Group G. Porto ended top after a 2-0 home win over Arsenal, who were second.
In Group F, Alberto Gilardino's header sealed a 1-0 victory for Fiorentina at Steaua Bucharest and a place in Europe's second-tier competition. Bayern Munich beat Olympique Lyon 3-2 to finish top of the table ahead of their French opponents.