Zubizarreta arrived at Marseille in October 2016 and was instrumental in the Stade Velodrome outfit securing Champions League football for next season with a second place finish after the 2019/2020 campaign was ended early because of the Coronavirus pandemic.
The 58-year-old former Spain and Barcelona goalkeeper parted ways with Marseille by mutual consent, and issued an emotionally charged farewell message.
"I want to thank Frank McCourt, Jacques-Henri Eyraud and Rudi Garcia for their confidence in me," Zubizarreta said. "It was a great joy to participate in a project as important as this one with OM.
"Thanks to André Villas Boas for having delighted me with his football and for becoming a true friend. Thank you to all the sporting staff with Albert Valentin on the front line, for your professionalism and pride. And what can I say of my players? And you, OM supporters? Thank you, thank you very much.
"We shared a project in which we experienced great joys and dark days, but in which I fought every day to do the best possible for the club minute by minute, hour by hour, and day by day ... behind the scenes or in full light, always trying to give my best.
"It is the project, this club, this city that have been in my heart and in my brain 24/7, because when there is so much passion around a club, it requires as much passion on a personal level, with feelings and energy.
"Thank you all for your confidence and your ability to always go forward. In Basque we say: "amaya da asiera" - 'the end is the beginning'. I close the door as Sporting Director and I begin as an OM supporter."
Marseille president Jacques-Henri Eyraud added: "Andoni is the first leader I recruited at the start of our project. It is therefore with great emotion that we part ways today.
"Since 2016, he has been by my side in all our battles. He was fully dedicated to bringing OM back to the heights it should be held to, and he always brought his expertise as we rebuilt the foundations for both the first team and the academy.
"Andoni is an honest man with great integrity. Beyond his immense role, he is a high-quality professional with whom I will always have a lot of fun talking."