The 35-year-old's contract will be terminated less than three months after he joined Sendai amid fanfare after spells at five other Japanese clubs.
"Having seen the damage caused by the disaster, Marquinhos has suffered psychological shock and has decided it would be difficult to continue playing under these circumstances," Vegalta said on their website.
Marquinhos helped Kashima Antlers to a hat-trick of Japanese championships from 2007-09, winning the golden boot in 2008, and has scored 109 goals in 230 J-League appearances.
Sendai was one of the worst-hit areas of the devastating 9.0 quake on March 11, although largely survived the enormous tsunami that followed and wiped out many coastal towns in northeast Japan.
More than 12,000 were killed with 15,000 still missing.
However, Vegalta will play their rescheduled opening J-League match on April 29, despite another large quake striking the area earlier this week.
