Villas-Boas will drive a Citroen C3 in the third tier of the championship for private crews in Portugal.
Villas-Boas, who joined the club in 2019, criticised the Marseille board for recruiting a player he had rejected.
"I offered my resignation, saying that I did not agree with the sporting policy," Villas-Boas said in a news conference.
"We ended the transfer window with a new player. He is a player that I had said 'no' for."
The 43-year-old has competed in Motorsports before, having took part in the Dakar rally in 2018. He had to pull out prematurely due to a back injury, having left Chinese side Shanghai SIPG in order to take part in the event.
The Rally Portugal, the fourth round of the WRC, will take place from May 20-23.