Rooney, who had already missed three clear-cut chances, gave Oldham the lead in the 15th minute with his first goal for the club, a fine glancing header.
Vale equalised in the 30th minute when Jennison Myrie-Williams cut in from the right and curled a delightful shot into the far corner.
The Valiants could have taken the lead in the 36th minute, but former Oldham striker Lee Hughes's penalty was saved by Mark Oxley. It was awarded after Hughes had been fouled by Jonathan Grounds.
In a remarkable opening period, in which both sides created numerous chances, the only surprise was that it produced only two goals.
Rooney struck for a second time as Oldham regained the lead in the 56th minute with a tap-in after a shot from Jonson Clarke-Harris was blocked.
Oldham sealed victory when James Dayton scored their third goal in the 76th minute, curling a shot into the far corner.