He was just 13 A-League games into a two-year contract.
Yorke's last game in charge was Friday's 1-0 loss away to Adelaide United.
The former Manchester United forward held a meeting with Macarthur chairman Gino Marra on Saturday where it was decided they would agree to mutually terminate his contract.
The Macarthur job was Yorke's first foray into management after a glittering playing career. He had achieved his coaching badges at United, where Sir Alex Ferguson was a mentor for him.
He won the Australia Cup - the Bulls' first piece of silverware - and picked up five wins in the league.
Yorke is now being linked with former club Sydney FC.