Anderlecht thumped 10-man Austrian champions Sturm Graz 3-0 while Bilbao went through after a 1-0 victory at Salzburg.
Paris Saint-Germain's record signing Javier Pastore gave them a 1-0 win over Slovan Bratislava and last season's top scorer in the competition Radamel Falcao, whose goals won the trophy for Porto, scored in Atletico Madrid's 4-0 drubbing of Udinese.
Last season's runners-up Braga hammered Maribor 5-1 while Larnaca, maybe inspired by fellow Cypriot side Apoel Nicosia's Champions League form, held Schalke 0-0 away, vying with Vaslui's 1-0 home win over Sporting as the upset of the night.
Guillaume Gillet put Anderlecht ahead midway through the first half in their Group L match and when Sturm's Ferdinand Feldhofer was sent off before the hour the hosts pulled away.
The competition's leading scorer, Matias Suarez, took his tally to six with a header after 74 minutes before Tom De Sutter added a third for the side that won the UEFA Cup in 1983.
PSG's Argentine midfielder Pastore scored with an exquisite volley, turning in Nene's cross from the left, just after the hour in Paris to keep the French side second in Group F.
Group leaders Bilbao, under former Argentina and Chile coach Marcelo Bielsa, stayed top and qualified when Ander Herrera's first-half goal gave them a narrow winy at Salzburg.
"I value the fact that we never stopped playing," said Bielsa, one of football's most eccentric coaches, whose side have quickly recovered from a poor start to the season.
Colombia striker Falcao, who hit a record 17 goals last season as he led Porto's victorious campaign, completed Atletico's drubbing of Udinese with a superb solo effort.
