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.
Adrian Lopez scored twice in the first quarter of an hour and Brazilian playmaker Diego added a third before halftime as Atletico joined Udinese at the top of Group I on seven points.
Larnaca, beaten 5-0 at home by Schalke two weeks ago, had the better chances in the return as they held out for a point although the Germans stayed top of Group J.
In the same group, former European champions Steaua Bucharest bounced back from a 5-0 loss at Maccabi Haifa to beat the Israelis 4-2 at home.
Held 2-2 at half-time and down to 10 men after Florin Costea was sent off, they still scored twice through Cristian Tanase to take the points.
A second-string Tottenham Hotspur side, also without manager Harry Rednapp who had minor heart operation on Wednesday, were knocked off the top of Group A after losing 1-0 at Rubin Kazan, where Bebras Natcho curled in a second-half free kick.
PAOK took their place with a 3-1 win at Shamrock Rovers
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