A fantastic treble from Rooney, complimented by a Cristiano Ronaldo tap-in, left Wanderers contemplating a first home defeat of the season as United left the Reebok just ahead of Chelsea on goal difference.
Rooney, who hadn't scored since his opening day double against Fulham, finished the game as a contest as early as the 16th minute when he put the Red Devils two up with successive finishes that were worthy of winning any game, before Ronaldo tapped in the third late on.
The match ball was claimed in time added on thanks to another cool finish when Rooney was clean through.
Although a fifth successive win and a first against their illustrious neighbours in the top-flight, would have put Bolton second, they never got going at all. They were never allowed to.
Rooney's first, in the tenth minute, was laid on a plate by Michael Carrick's calculated chipped through ball that split defenders Abdoulaye Faye and Nicky Hunt. All Rooney had to do was fire past a hapless Jussi Jaaskelainen at his near post.
His second arrived just six minutes later when capitalised on an unfortunate ricochet from Tal Ben Haim's block tackle on Gary Neville. The ball squirmed to Rooney who controlled and curled it into the bottom right corner. Again Jaasekelainen had no chance.
The opening 20 minutes were as one sided as any Premiership game could ever be - especially by an away side - and the game was done and dusted.
Although Rooney's goals were key, Ryan Giggs was also instrumental down the wing with a couple of dangerous crosses and a volley well saved by Jaaskelainen. Bolton were awarded their first attacking position thanks to a free-kick 25 yards from goal in the 23rd minute.
Captain for the day Gary Speed, replacing the suspended Kevin Nolan, stepped up and fired it wide of the left upright with Edwin Van der Sar always in control of the situation.
From then on, United stepped off the gas, content with their two-goal lead, and it was soon evident that Bolton had absolutely nothing to throw back at them.
Ivan Campo tried his best to orchestrate things from the centre of midfield and Nicolas Anelka, starved of any goal chance, looked Bolton's best bet wide on the left.
For a short spell midway through the second half, Bolton were able to revert to their normal tactics of pumping long throws and crosses into the box, but defensive duo Rio Ferdinand and Nemanja Vidic stood strong and repelled the danger.
And then it was back to the goals, and the icing on top of the cake. United played so well in this derby that it would have been an injustice if they had left with only two goals to their name. They really did play that well in scoring the first goals at the Reebok this term.
So when Louis Saha unselfishly fed Ronaldo in the 84th minute, following another fine assist from Carrick, it was no surprise to see him roll the ball into an empty net, which Jaaskelainen had vacated expecting Saha to shoot.
And to round things off in the most perfect of fashions, Rooney cushioned Darren Fletcher's through ball, following a loose ball from Ivory Coast international Abdoulaye Meite to fire past the keeper.
It was Rooney's first treble in the Premiership and his second for the Old Trafford side after the one he got on debut in the Champions League against Fenerbahce in October 2004.