Brian McPhee scored a quick-fire first-half double at Creamery Park before Graeme McLaren added a third before the break.
Greg Meikle pulled a goal back for the Fifers in the second half.
Also in the Super League, Linlithgow Rose, who are looking to finish as runners-up to Bo'ness, were deadlocked with Hill of Beath Hawthorn at half time.
The Prestonfield clash erupted after Gordon Herd had made the breakthrough for Rose early in the second half when the home side's John Ward and Haws' Andy Roberts were both sent off.
Roddy McLennan then scored a second for the Scottish Cup winners, who rested several regulars ahead of Saturday's East of Scotland Cup final against Musselburgh.