Zubizarreta previously served the same role at Barcelona and helped recruit Neymar and Luis Suarez.
Zubizarreta previously served the same role at Barcelona from 2010 to 2015 and helped the Spanish champions recruit Neymar and Luis Suarez.
His appointment comes a day after Marseille parted company with Belgian sporting director Gunter Jacob as the club's new owner, American tycoon Frank McCourt, continues his overhaul of the nine-time French champions.
"Marseille has a big heart, a great football soul like Athletic Bilbao and Barcelona," said Zubizarreta, referring to two of his former clubs.
"There's a great passion with the supporters in Marseille, it's a huge opportunity for me football wise as well as individually."
The Spaniard will work alongside new coach Rudi Garcia after the former Lille and Roma boss signed a three-year contract to take over at the Stade Velodrome last week.
Now 55, "Zubi" won 126 caps for Spain during a distinguished playing career in which he represented Athletic Bilbao, Barcelona and Valencia.