The striker tapped in after his header from Nani's cross rebounded off the post back into his path on 34 minutes.
Ben Foster made a brilliant stop to deny Christian Benitez a goal on his Birmingham debut in the 77th minute.
Substitute Michael Owen missed a chance to open his account for United when he shot at Joe Hart in stoppage time.
Deprived of first-choice centre-backs Nemanja Vidic and Rio Ferdinand, who will have a scan on Monday on a calf injury sustained in training, United boss Sir Alex Ferguson moved John O'Shea into central defence alongside Jonny Evans, with Fabio da Silva promoted to right-back.
Paul Scholes returned to the centre of midfield, while new signing Antonio Valencia slotted into the sizeable hole vacated by Ronaldo on the right.
Rooney came close to his 100th goal in the 83rd minute, but Owen should have put the result beyond doubt when he was released through the middle by Rooney's chested flick.
But one-on-one with Hart, the striker's effort deflected off the goalkeeper's leg for a corner.
In the end, that one goal from Rooney was enough to bag all three points and provide the perfect response to Chelsea and Arsenal's victories in this opening weekend of a long hard season.
Foster, Fabio, O'Shea, Evans (Brown), Evra, Valencia, Scholes, Fletcher, Nani (Giggs), Rooney, Berbatov (Owen).
Kuszczak, Anderson, Gibson, De Laet.
Venue: Old Trafford.
Source: BBC Sports & manutd.com
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