The 29-year-old had been sidelined by Hammers boss Slaven Bilic since refusing to play against Crystal Palace on January 14.
A number of bids for the French international were rejected by the Premier League side, who were keen to hold onto their talented midfielder, before agreeing to let him leave for £25million.
A brief statement from West Ham read: "West Ham United can confirm that the Club has today agreed a fee of £25m for the transfer of Dimitri Payet to Olympique de Marseille."
Payet had joined Bilic's side for £10.7m in 2015 and scored 12 goals in his first campaign before signing a new contract until 2021, but with the club struggling for form this term, he opted rather to join his former Ligue 1 side - having cited personal reasons for the move.