Ronaldo, sent off during United's 3-1 defeat at Eastlands in January 2006, was dismissed by referee Howard Webb for two yellow cards in the space of nine second-half minutes for a foul on Shaun Wright-Phillips, followed by a deliberate handball offence.
With United also collecting five other yellow cards, the club can expect an FA fine for failing to control their players, but this victory will overshadow any such disciplinary issues.
City manager Mark Hughes had the distinct disadvantage of sending his players into derby action having only returned from the Uefa Cup trip to Schalke in the early hours of Friday morning. With United enjoying the luxury of two extra days to prepare, it was perhaps unsurprising that they dominated the first-half.
United have started well on several occasions this season, however, and failed to take advantage of their dominance and, with a series of chances wasted in the early stages, a repeat of the disappointing results against Liverpool, Everton and Arsenal - when United failed to build on strong starts - threatened to rear its head once more.
Such was their stranglehold on the game early on, United should have been two goals ahead inside the opening quarter of an hour. However, Darren Fletcher and Cristiano Ronaldo both spurned clear chances to let City off the hook.
When Dimitar Berbatov's glancing header from Rafael's cross was brilliantly saved by Joe Hart on 23 minutes, the frustration and growing anxiety was evident on the United bench and Sir Alex Ferguson's mood would not have improved when Stephen Ireland struck the post following a weak punch by Edwin van der Sar on 32 minutes.
The breakthrough that United deserved came three minutes before half-time, however, when City's failure to clear the danger inside their own penalty area resulted in Michael Carrick aiming a left-foot strike goalwards.
Hart saved the shot, but the loose ball dropped at Rooney's feet and the England forward gleefully scored from six yards to break the century mark in club football.
Although City raised their game after the break, United continued to dominate and the home side did not come close until Van der Sar saved well from Richard Dunne deep into stoppage time.