Rooney gave United the lead in first-half stoppage time but then gifted Hull a route back with the mistake that led to Craig Fagan’s penalty equaliser.
The striker then forced an own goal from Andy Dawson and set up a third for Dimitar Berbatov.
The victory lifted United back above Arsenal into second and within two points of leaders Chelsea.
United welcomed back Rafael da Silva, Wes Brown and Nemanja Vidic and they were ahead when Rooney tapped home.
But Hull were level when Rooney gave the ball away and Rafael shoved Jozy Altidore allowing Fagan to score from the spot.
Rooney then slid a ball across the box which Dawson (73) turned home and Berbatov (82) tapped in after another pass from Rooney.