Chairman Ambrose Rachier has confirmed to P Live the receipt of a resignation letter from the Brazilian coach, who joined the club in 2016.
"I have received the resignation letter from Ze Maria. He has simply thanked us for the time we were together and wished us well. He never cited any reasons for his decision and we now have no option other than to part ways with him.
"He is departing together with his assistant coach Marco Aurelio while keeper trainer Sandro Fantoni is remaining," he told P Live.
Ze Maria, whose shocking exit comes four days after they lifted the 2017 SportPesa Super Cup trophy in Tanzania, leaves Gor Mahia at the top of the table with 27 points from 13 matches.