The French giants have the option of making Guendouzi’s move permanent at the end of the 2021/2022 season.
Guendouzi joined Arsenal from Lorient in the summer of 2018 and made 82 appearances in total for the Gunners before falling out of favour under Mikel Arteta towards the end of the 2019/2020 season.
The 22-year-old spent last season on loan in the Bundesliga with Hertha Berlin, where he scored two goals in 24 league appearances to help the club escape relegation.
A Marseille statement confirming the move said: "Guendouzi is a modern midfielder, technically strong and with good passing quality.
"A player of character, he has a good vision of the game. These qualities he will undoubtedly be able to share with the Olympic Marseille team."
Guendouzi bid a fond farewell to Arsenal after the move was confirmed with a tweet that looks like he could have played his last game for the club.
"Thank you Arsenal, thanks for everything!" Guendouzi posted in the first of a series of tweets.
"I discovered and learned so much during my time here. It would be impossible to list everything without forgetting one memory or word… but I will never forget any minute spent with the Gunners jersey.
"I will never forget the Emirates Stadium. I will never forget the fans. I will never forget the city. I will never forget everything I've been through here. I will never forget that my only will was to defend with pride Arsenal colours.
"Thanks to all of those who believed in me during my time here, during the good and the bad moments. I can only wish the best to the club and its fans who deserve so much, trust me! Goodbye Arsenal, I will never forget you and will be a Gooner forever."
