The agreement includes an option for Marseille to purchase the Spanish centre-back on a permanent basis.
It is the first time the 29-year-old has played outside his homeland and he will be tasked with shoring up a defence that shipped 52 goals in Ligue 1 last season.
His arrival comes as a welcome boost for ex-Chelsea boss Villas-Boas, who has endured a difficult few weeks since replacing Rudi Garcia.
Marseille lost 2-1 to Accrington Stanley in a friendly in Manchester and were then routed 4-0 by Rangers at Ibrox.
Star striker Mario Balotelli left the club on a free transfer at the end of last term.