Tal Ben Haim was left cursing his luck as Bolton exited the UEFA Cup after losing 2-1 in Marseille.
The Israel captain steered the ball into his own net after 68 minutes following a cross from Habib Beye.
Yet Bolton had taken the lead in this second leg of the last 32 through Stelios Giannakopoulos, only for Franck Ribery to pull Marseille level.
Defeat meant Bolton missed out on a meeting with Zenit St Petersburg in the last 16 after they overcame Rosenborg.
Bolton manager Sam Allardyce took charge of the squad for this UEFA Cup game even though he was still suffering from a chest infection.
Allardyce flew in this morning, with assistant boss Sammy Lee going through the pre-match preparations.
Bolton showed two changes from the team which drew against West Ham, with Bruno N'Gotty and Abdoulaye Faye replacing Radhi Jaidi and Hidetoshi Nakata.
Bolton almost got off to a perfect start in front of a hostile crowd as Kevin Davies was flattened by Frederic Dehu in the fifth minute.
Jay-Jay Okocha saw his free-kick take a deflection off the wall but goalkeeper Fabien Barthez managed to parry the ball to safety.
Bolton goalkeeper Jussi Jaaskelainen showed a safe pair of hands in the ninth minute to gather safely a corner from Ribery.
Marseille stepped up the pressure and Samir Nasri went close before Beye headed wide from a good position.
Bolton made the breakthrough after 25 minutes following a mistake by former Manchester United goalkeeper Barthez.
There seemed to be little danger when Okocha launched the ball forward but Barthez, under no pressure, flapped at the ball and Giannakopoulos steered it into an empty net.
It was Stelios' ninth goal of the season and his first in Europe in this campaign.
Marseille certainly looked edgy and nervous in front of their home fans, although they continued to be dangerous on the break and Lorik Cana found the side netting from an acute angle in a quick breakaway.
Bolton responded immediately and Joey O'Brien released Stelios with a glorious long ball. The Greek winger took it first time but Barthez was able to make the save.
Marseille hit back and Wilson Oruma rattled in a shot from 20 yards that was parried by Jaaskelainen.
Then Faye found the net for Bolton only for his effort to be ruled out for offside, and he picked up a yellow card for his trouble after slotting home when the whistle had gone.
Marseille drew level in first-half stoppage-time when Ribery got in front of Stelios to head the ball home.
Marseille had grown in confidence after getting the equaliser and Oruma strode forward in the 47th minute only for his shot to go over the bar.
Then, three minutes later, Nasri stung the hands of Jaaskelainen with a shot from distance. This was a testing spell for Bolton and Nasri then dragged his shot wide as they stepped up the pressure.
Marseille were beginning to knock the ball around but Bolton were still in the driving seat with that away goal in the bag. However, Ribery was becoming increasingly influential and the game was beginning to run away from Bolton.
Marseille went ahead in the 68th minute when Ben Haim steered the ball into his own net following a cross from Beye. It was a major setback for Bolton considering how well they had played.
Henrik Pedersen was given his first run-out since October, after an Achilles injury, when he came on for Faye in the 73rd minute.
However, Pedersen lasted only 13 minutes after a stiff challenge from Cana which earned him a booking.
It was Marseille who looked like adding to their tally with Oruma and Nasri both sending shots wide of the post late on.
Bolton continued to push forward but could not get their vital goal and their first campaign in Europe came to an end in the south of France.
