"I've decided to leave," said Garcia during a press conference ahead of Marseille's final game of the season against Montpellier while seated next to club president Jacques-Henri Eyraud.
"I proposed this option to the club president and he has accepted it."
Marseille finished the 2016/17 season in fifth place and qualified for the Europa League.
Garcia, who played for Lille and Caen during a nine year playing career, steered Marseille to the Europa League final in 2018 where they were beaten by Atletico Madrid.
During his last campaign at the club, Marseille appeared to be in the mix for a berth in next season's Champions League but they were unable to sustain their challenge and will finish the season fifth or sixth - 30 points off the champions Paris Saint-Germain.