The former Liverpool winger's departure comes less than two months after Yokohama lost to Al Ain in the Asian Champions League final.
Kewell, who had limited managerial experience prior to taking the job, was appointed in late December to replace Kevin Muscat and was the third consecutive Australian in the post.
Predecessors Ange Postecoglou and Muscat led Marinos to the J League title in 2019 and 2022 but the club's form under Kewell has been inconsistent and they are currently 12th, 20 points adrift of leaders Machida Zelvia.
Their 4-1 win over Kashima Antlers on Sunday came on the heels of four straight league losses.
Kewell will be replaced on an interim basis by John Hutchinson, who has worked as the club's head coach since the turn of the year.