Former Leeds and Liverpool forward Kewell's side lost to Hernan Crespo's Al Ain over two legs in Asia's Champions League final but Yokohama have been poor in the J. League and lie 12th in the 20-team table.
Yokohama said the Australian had been dismissed with immediate effect and assistant coach and fellow Australian John Hutchinson would take over on a temporary basis.
Kewell joined Yokohama at the start of the year in the latest stop of a coaching career that has failed to live up to his successes as a player.
The 45-year-old struggled in lower-league English football with Crawley Town, Notts County and Oldham, and he was sacked by fifth-tier Barnet in 2021 after failing to win in his first seven matches.
He looked to have turned the tide when he took Yokohama to their first AFC Champions League final.
But he paid the price for Yokohama managing just eight wins in 23 J. League games, losing 10 with five draws.
Kewell succeeded fellow Australians Ange Postecoglou and Kevin Muscat as Yokohama coach.
His previous job was as a first-team coach at Celtic under Postecoglou, who has since moved on to Tottenham in the English Premier League.
