South End opened the scoring through Ahmed Boudissa before AR Elite responded.
Ahmed Boudissa put Manchester South End ahead in the Premier Division fixture.
AR Elite then took control, with Anis Bunajah scoring from a free kick and a penalty.
Both teams added one further goal as AR Elite completed a 3-2 victory.
The result moved AR Elite to the top of the Premier Division.
Oldham Hulmeians moved into second place after winning 5-3 away at Chadderton Cott in another of the division’s fixtures.
Bedians and Wythenshawe Wanderers shared the points in a 3-3 draw, while AFC Urmston Meadowside Redstar recorded an 8-0 victory at Winton Wanderers.
