The game was decided by a 59th-minute penalty. Ronaldo made one of his characteristic darting runs into the Bolton area where his progress was halted by a tackle from Jlloyd Samuel. When Rob Styles pointed to the spot, the Bolton players reacted with disbelief thinking Samuel's tackle was well timed.
After scoring on his first start of the season against Middlesbrough in the midweek League Cup tie, Ronaldo did not require a second invitation to repeat the feat, easily beating Jussi Jaaskelainen from the penalty spot.
The game was put well beyond Bolton's reach in the 77th minute when Rooney, relegated to the bench as part of Sir Alex Ferguson's squad rotation policy, collected a pull back from Ronaldo and steadied himself before driving in a superb finish, his first United goal since the end of April.
The outcome had seemed inevitable over the opening hour, given United's domination and the work required of Jaaskelainen and his defence, but the manner of their opening goal was highly debatable.
With Rooney on the substitutes' bench, and Dimitar Berbatov starting for the first time at Old Trafford, United did not take long to find their attacking stride.
After two early half chances for Ronaldo, Jaaskelainen was required to dive smartly to his right to deny a Berbatov header from Gary Neville's 13th minute deep cross although the keeper was not quite as tidy soon after in dealing with Carlos Tevez's long strike, spilling the ball and watching in relief as Park Ji-sung could only turn the rebound into the side netting from a difficult angle.
Ronaldo might have got off the mark after 20 minutes but Jaaskelainen made another full-length diving save from his 24th minute, 25-yard free-kick.
Johan Elmander, Gavin McCann and, predictably, Kevin Davies, were booked as the pressure mounted, Ronaldo's near-post free-kick providing Jaaskelainen with yet another test before Darren Fletcher's perceptive pass picked out the unmarked Anderson, whose carefully weighted shot just cleared the bar.
The best, prolonged spell of United possession ended with a chip from Tevez which was headed to Rio Ferdinand by Berbatov, presenting the defender with a shot which Jaaskelainen, again, saved well.
Yet, for all United's relentless pressure, the half would end with Bolton missing a golden chance best chance from Gretar Steinsson's right-wing cross.
Davies and Ferdinand, sliding in together, missed the ball and the unmarked Fabrice Muamba had the apparently simple task of converting from a dozen yards only to miscue his shot horribly, sending the ball well wide.
Ricardo Gardner had a glimpse of the United goal soon after the restart, shooting narrowly wide after United could only half-clear an Andy O'Brien free-kick but the home side did not need long to re-apply the pressure.
A Neville cross was miskicked by O'Brien and collected by Ronaldo whose cheeky, prodded shot found a path through a crowded area and struck the foot of the Bolton post.
The penalty decision followed soon afterwards, taking with it Bolton's hopes, and the introduction of Rooney and Paul Scholes, in a 71st minute double substitution, underlined the uphill battle they faced.
Sure enough, Rooney's goal six minutes later put the contest to rest and his fellow substitutes Nani and Scholes, twice, should have added to the lead.