The home side opted to play the match behind closed doors in response to league officials turning down their request for it to be postponed because of a host of Covid-19 cases in the Bordeaux squad.
Only 5,000 fans are permitted at football matches under new government restrictions introduced to try and curb spiralling daily infection rates fuelled by the Omicron strain of the virus.
Bordeaux on Wednesday said they had 17 players unavailable. They have returned 21 positive test results over the past three weeks and were forced to field several reserve-team players in their French Cup game last weekend, which they lost 3-0 at Brest.
The win for Marseille was their first in Bordeaux in 37 attempts and sent Jorge Sampaoli's team above Nice into second place, 10 points back of leaders Paris Saint-Germain.
"We are indeed very satisfied to end this long run," said Sampaoli.
"It's a great success so congratulations to the players. It was well-known and we were made to understand it everywhere we went."
Bordeaux sit just one point above the relegation play-off place. They have won only three times in 20 league matches under former Switzerland coach Vladimir Petkovic this season.
