"I've decided to leave. I proposed this solution to my president (Jacques-Henri Eyraud), who accepted it," Garcia, who joined the club in Oct. 2016 from AS Roma, told a news conference.
"If I only listened to my determination and my ego, I would stay but if I listen to my commonsense and my reason, I have to stop. Why? Because I believe enormously in this project.
"In two and a half years, I was part of this project and, for the sake of it, I think it's better that I leave now. It has been a great pleasure to coach OM."
After a lukewarm start to the season, Marseille's form got worse and they finished bottom of their Europa League group.
Marseille's nightmare run continued on the domestic front as were knocked out of the French Cup by fourth division Andrezieux in January, with Garcia attracting widespread criticism.
A 3-0 home league defeat by Olympique Lyonnais earlier this month ended Marseille's hopes of playing in European competition next season as they could not longer finish in the top four.
"There are few jobs as difficult as coaching. It is a job that requires an exceptional character," Eyraud said.
"I have a lot of respect for Rudi. He will remain forever as the coach who brought Marseille to the European final."
Garcia's final game in charge of Marseille will be a league encounter at home to Montpellier on Friday.
(Reporting by Hardik Vyas in Bengaluru; editing by Ken Ferris)
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