The France international was frozen out of the squad under Mikel Arteta due to disciplinary reasons but established himself as an integral figure in the Olympiens midfield last season.
Guendouzi amassed five goals and 14 assists in 55 appearances for Marseille in all competitions, helping Jorge Sampaoli's side return to the Champions League with a second-placed finish in Ligue 1.
Marseille were always expected to make the 23-year-old's stay a permanent one, and the Gunners have now confirmed that Guendouzi has left the club for good to return to his homeland.
Arsenal will reportedly receive just £9.5m for Guendouzi's sale, and the former Lorient youngster has signed a three-year deal with the now-managerless Olympiens.
Guendouzi was signed by Unai Emery for £7.2m for Arsenal in the summer of 2018, and the midfielder leaves the club after scoring one goal and setting up five more in 82 matches.
Following a bust-up with Brighton & Hove Albion's Neal Maupay in the 2019-20 season, Guendouzi lost the trust of Arteta and was also shipped out on loan to Hertha Berlin.
Guendouzi did collect an FA Cup winners' medal with Arsenal after playing three games for the team en route to the 2020 trophy, and he follows the likes of Alexandre Lacazette, Konstantinos Mavropanos, Dan Ballard and Jordi Osei-Tutu out of the exit door.
However, Guendouzi has arrived at Marseille in the wake of Sampaoli's shock exit from the club, with the 62-year-old departing after less than 18 months in charge at the Orange Velodrome.
"Olympique de Marseille and Jorge Sampaoli announced their joint decision to end their collaboration. Jorge Sampaoli is the first coach to whom Pablo Longoria entrusted the fate of the first team in February 2021," a statement read.
"Since his first day in Marseille, he has fully invested in the implementation of a philosophy of play and a winning state of mind corresponding to the values of Olympique de Marseille. It is therefore with emotion that the club and Jorge Sampaoli announce their joint decision to end their collaboration.
"OM would like to sincerely and warmly thank the work of Jorge Sampaoli. After 16 months of collaboration, this work has allowed the club to reach a milestone in the construction of its new sports project and to qualify directly for the UEFA Champions League.
"We are satisfied with the path we have taken and the emotions we have experienced together, but after a long reflection, both parties, acting in the interest of the Olympique de Marseille project, have agreed to end this stage."
Sampaoli took charge of just 66 matches for Marseille, winning 36 of them, and he admitted on social media after his exit that his "rhythm and objectives" did not align with the club's hierarchy.
Marseille have also captured Sead Kolasinac from Arsenal this year, but their efforts to strike a permanent deal for Ligue 1 Young Player of the Year William Saliba will seemingly end in failure. body check tags ::