Rooney netted his first goal of the season after 20 minutes with a neat finish, running on to a clever through ball from Memphis Depay.
He doubled the lead four minutes after halftime following a flowing move and grabbed his third just before the hour in Belgium courtesy of a cute pass from Juan Mata.
Ander Herrera added a fourth goal as United, 3-1 up after the first leg, eased through to the group stage of Europe's premier club competition 7-1 on aggregate.
(Reporting by Ed Osmond; Editing by Greg Stutchbury and Pritha Sarkar)
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