The French club's erratic goalkeeper gifted Wanderers a 25th-minute lead in the round of 32 second leg encounter at the Stade Velodrome, with Stelios Giannakopoulos' effort also putting them ahead on aggregate after last week's goalless draw in Bolton.
However, Marseille, inspired by the outstanding Franck Ribery, hit back with a Ribery header on the stroke of half-time and a Tal Ben Haim own goal, to set-up a meeting with Zenit St Petersburg in the next round.
Wanderers made a great start and were almost ahead inside five minutes when a deflected Jay-Jay Okocha free-kick nearly caught out Barthez, but the former Manchester United shot-stopper just managed to get across to keep it out.
Marseille were soon into their stride and looked set to turn up the pressure when Barthez's gaffe presented Wanderers with the lead.
An Okocha cross from the right flank should have been easy for the goalkeeper to deal with, but he spilled it under little pressure and Stelios seized on the loose ball and steered it beyond the two defenders on the line.
The home side pushed forward with Ribery at the centre of everything they did, but Sam Allardyce's men got back in numbers to deny them a clear sight of goal.
Marseille, however, looked vulnerable to the counter attack and some better timed runs from midfield would have created two golden chances for Bolton, but Abdoulaye Faye and Kevin Nolan both strayed offside at vital moments.
It looked as though the visitors would go in ahead but their defence was caught out on the stroke of half-time, when Ribery found space between Stelios and Bruno N'Gotty ten yards out to head home a Samir Nasri cross.
Boosted by the equaliser, Marseille came out strongly at the start of the second half and Wilson Oruma fired over the crossbar from distance before Jussi Jaaskelainen had to get down to save from Nasri.
The impressive Nasri hit a shot two yards wide from the edge of the area after some neat build-up play, as the Mediterranean giants set-up camp in the opposition half.
With 68 minutes on the clock Marseille's pressure finally paid off. Stelios misjudged a long ball and allowed it to bounce behind him, giving Habib Beye time and space to cross.
Beye's wicked delivery across the six-yard box left Jaaskelainen stranded and Ben Haim turned it into his own goal as he tried to prevent it reaching Mamadou Niang.
Wanderers looked to hit back immediately and within seconds of the restart Nolan had a great chance to score, but Barthez blocked his effort.
Bolton poured forwards in numbers and substitute Henrik Pedersen was just inches away from heading home, but the hosts remained dangerous on the break and a shot from Nasri was deflected wide for a corner.
The night finished with another blow for Bolton when Pedersen, who was making his first appearance since October, was stretchered off after suffering an ankle injury in a bad foul by Lorik Cana.