Sunderland came away from Old Trafford with a 1-0 victory in the wake of David Moyes' departure as United manager last season, and early openings on Saturday for visiting forwards Connor Wickham and Jermain Defoe suggested the hosts were in for a similarly uncomfortable afternoon.
Ashley Young had a first-half effort diverted against the crossbar by John O'Shea, before the visiting captain and his fellow former United defender Wes Brown found themselves at the centre of the game's decisive moment in the 64th minute.
Last man O'Shea hauled back Radamel Falcao to concede a clear penalty, with Brown in close attendance - although referee Roger East showed the latter player a red card to prompt protests and bemusement from the Sunderland contingent.
Rooney - starting up-front as Louis van Gaal made five changes to his starting XI - converted from the spot and added an 84th-minute second to ensure United bounced back from a 2-1 defeat to Swansea City last time out, keeping their bid for UEFA Champions League qualification on track.
Rooney headed a corner wide at the near post in the fourth minute as United made an encouraging United start, although Sunderland soon fired two early warnings of their own.
Wickham, one of three players recalled by Gus Poyet following last week's goalless draw with West Brom, raced towards a backpeddling home defence and drew an excellent low save from David de Gea.
Defoe curled a strike narrowly over in the seventh minute.
Back came United, and Young drove a shot over the crossbar when Lee Cattermole partially cleared, before Defoe failed to trouble De Gea with a 16th-minute chance.
An unsettled home crowd almost had something to cheer when Young hit Antonio Valencia's right-wing cross goalwards at the back post, but O'Shea slid in to divert the ball against his own crossbar.
That 25th-minute opportunity prompted an increase in tempo from United, but they were unable to find the breakthrough before half-time.
Van Gaal sent his side out early for the second period and replaced the ineffective Angel Di Maria with Adnan Januzaj.
Sunderland found themselves under set-piece pressure after the resumption, with Marcos Rojo lashing a shot over from Falcao’s knockdown.
Januzaj then sent a rasping 20-yard effort wide following a poor headed clearance from Anthony Reveillere, before East made an unlikely hash of a relatively straightforward penalty situation.
Rooney kept his calm to pick out the bottom corner from 12 yards.
Sunderland goalkeeper Costel Pantilimon was a busy man as United poured forward during the closing stages and, when he could only parry another firm Januzaj strike, Rooney was on hand to head home his second and ensure Sunderland's winless Premier League run extended to four matches.
