Joyce's departure was announced on Wednesday after the conclusion of his two-year contract with the Australian club.
Former Wigan Athletic manager and Manchester United reserve team boss Joyce oversaw Sunday's 1-0 extra-time loss to Adelaide United in the Elimination Final.
"It's been a challenging couple of seasons, but I have great pride in the players and staff for the progress the club has made," Joyce said.
"I've seen real growth from the playing group and within the football organisation and the continued development of the right kind of culture. I am confident that A-League success is around the corner for the club. I'd like to wish everyone at the club and the fans the best of luck for the future."
City – bankrolled by the City Football Group – turned to Joyce in 2017 after John van 't Schip's resignation in January that year.
During his time in Melbourne, Joyce guided City to third- and fifth-place finishes in the regular season.
"Warren leaves Melbourne City FC having helped the club progress against many of our organisational ambitions, and we are grateful for his dedication and passion for the club's development over the past two years," City chief executive Brad Rose said.
"In particular, under his stewardship a significant number of young players have made the transition to first-team football and many have been recognised with national team selection."