A 1-1 draw at the Petrovsky stadium sealed a 2-1 aggregate success for Russia's Zenit who reached the last eight for the first time.
Germany's Schalke 04, the 1997 winners, Steaua Bucharest, Basel and Levski Sofia also advanced. Schalke are the only side from the eight teams who dropped out of the Champions League into the UEFA Cup to reach this stage.
Middlesbrough, Rapid Bucharest and Sevilla qualified for the last eight on Wednesday with Boro knocking out Italy's AS Roma and Rapid overcoming Bundesliga high-flyers Hamburg SV.
Marseille's reserve keeper Cedric Carrasso, deputising for the injured Fabien Barthez, had a game to forget.
His blunder allowed Aleksandr Kerzhakov to fire Zenit ahead and he was sent off in stoppage time for a crunching challenge on the same player.
Carrasso spilled Kerzhakov's speculative shot which then hit the post before trickling over the line in the 69th minute.
Marseille, the beaten 2004 finalists, quickly levelled through defender Frederic Dehu's free kick but Zenit held firm for the final 16 minutes.
"The main thing for us tonight was to keep a clean sheet. Still, we had more chances than them and I'm proud of the way we fought," said Zenit's Czech coach Vlastimil Petrzela.
STEAUA CRUISE
Romania will boast two sides in the last eight after Steaua, the 1986 European Cup winners, underlined their title credentials by crushing Real Betis 3-0 in Spain to go through by the same score.
Midfielder Banel Nicolita got the opener on 54 minutes and Betis winger Joaquin was shown a red card for elbowing Nicolae Dica in the face six minutes later.
Victoras Iacob headed the second after 78 minutes and Nicolita added a third as Betis, facing a survival battle in Primera Liga, fell to pieces.
Schalke, 1-0 down from the first leg, were helped on their way to a 3-0 win in the return when Palermo captain Eugenio Corini was sent off for stopping Mladen Krstajic's shot with his hands on the goalline late in the first half.
Georgian international Levan Kobiashvili placed his penalty down the middle as Mariano Andujar dived to his left to send the Bundesliga side in front at halftime.
Two goals in the final 18 minutes sealed Palermo's fate. German international forward Gerald Asamoah crossed for Dane Soren Larsen to head in, then set up Mimoun Azaouagh to rifle in a third.
Any hopes Ligue 1 strugglers Strasbourg had of overturning their 2-0 first-leg defeat were effectively killed off when Brazilian striker Eduardo scored for Basel in the third minute.
Striker Rudy Carlier hauled Strasbourg level seven minutes later but Eduardo struck again in the first half. Cedric Kante's late goal earned Strasbourg a 2-2 draw.
Croatian defender Igor Tomasic headed Levski Sofia into the quarter-finals as the Bulgarians beat Udinese 2-1 to go through by the same score on aggregate.
Tomasic scored with a glancing header from Lusio Vagner's cross in the 63rd minute, completing a fine fightback after the Serie A side had gone ahead.
Levski, unbeaten at home in the competition this season, trailed to Argentine Fernando Tissone's goal midway through the first half but midfielder Daniel Borimirov levelled from Sedrik Bardon's cross on 52 minutes.
The final is in Eindhoven on May 10.
