The striker took his tally in the SPL to 17 goals in what is proving to be an outstanding campaign and Derek McInnes' side held on for all three points despite Barry Robson's red card 18 minutes from time.
Rooney turned in a Mark Reynolds cross six minutes before half-time and United were unable to respond, as second-placed Aberdeen secured a third consecutive win to strike a blow to the visitors' own European aspirations.
Midfielder Robson was shown a straight red card against his former club for clashing with Charlie Telfer, but his dismissal did not prove to be costly.
Fourth-placed United rarely threatened and are now 22 points behind Aberdeen with six matches remaining.
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