Speaking at a press conference ahead of his side's final game of the season at home to Montpellier on Friday, and sitting alongside president Jacques-Henri Eyraud, Garcia, quoted by France Football,said: "I have decided to leave."
Garcia, 55, who had signed a contract extension in October through to the end of the 2020-21 season, added:"Iproposed this solution to my president, who accepted it.
"If I listen to reason, I must stop this adventure.For the good of the project, it is better that we separate now."
Just a year ago Garcia led Marseille to the Europa League final, only for his men to be beaten 3-0 by Atletico Madrid.
This season the club bowed out of the competition at the group stage, embarrassingly lost to National 2 side Andrezieux in the Coupe de France, and can finish no higher than fifth in the league this season, therefore missing out on European football next term.
Eyraud said:"I have a lot of respect for Rudi.He will remain forever as the coach who brought OM to the European final."