Kisnorbo becomes the second coach to leave the club this season, having been promoted to the role, initially on an interim basis, after Steve Holland was sacked in April.
The club issued a statement on Thursday saying Kisnorbo was leaving by mutual agreement due to personal reasons, with Hideo Oshima to take charge of the team on an interim basis.
The Australian had struggled to turn the team's fortunes around, winning two and losing eight of his first 10 matches in charge and they sit last on the 20-team J1 League ladder.
Kisnorbo was quoted in the club statement saying: "Due to personal reasons, the club and I have mutually agreed that it is in the best interest of all parties - my family, the club, the fans, the staff, and the players - that I part ways with Yokohama F.Marinos.
"We have worked together to ensure this transition is handled smoothly and amicably."
Former Socceroo defender Kisnorbo joined the club as an assistant in December, having walked out on a three-year deal as Melbourne Victory coach after just seven games.
The ex-Melbourne City premiership-winning coach had returned to Australia following a difficult year at the helm of French club Troyes, who were relegated from Ligue 1 following his November 2022 arrival.
That tenure ended with his departure in late 2023 after Ligue 2 Troyes had won just two of 15 matches.
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