The result means United have completed their best-ever start to a Premier League season, while Rooney took his personal tally to eight in four games, part of an overall team tally of 18, 13 of which have come in the last two matches.
Indeed, aside from Manchester City, Rooney has now scored more league goals on his own this season than any of the clubs attempting to keep pace with this unbelievable start, in which one city appears to have annexed the entire championship between them.
Hernandez marked his first start of the season with two goals, although on a night when everyone in red played their part, it was a dazzling run from teenager Phil Jones to create Rooney's second which sparkled the most.
Indeed, the only downside for Sir Alex Ferguson ahead of another Champions League quest getting under way against Benfica on Wednesday was the suspected broken foot midfielder Tom Cleverley sustained in an early collision with Kevin Davies, and an injury to Jonny Evans.
Although he endorsed David de Gea yesterday, it was claimed Ferguson was having extreme doubts over whether to drop the 20-year-old into the maelstrom of the Reebok Stadium, even now Owen Coyle has smoothed off quite a lot of that infamous abrasive edge.
As it turned out, the United boss need not have worried.
It was first-half stoppage time before Bolton produced a cross that tested De Gea's mettle, by which time the visitors were three up, with the only doubt over victory concerning how many they would get.
Four minutes was all it took for United to rediscover the scoring form that devastated Arsenal a fortnight ago.
Nani danced down the right wing and when he flashed over a low cross, Hernandez left Gary Cahill standing with some exemplary movement before nicking the ball home at the near post.
Davies tried to lead by example but a crunching tackle on Cleverley, which led to the young midfielder's early exit and quite possibly a lengthy absence from the game, and an equally forceful challenge on Patrice Evra, which earned the veteran striker his 100th Premier League caution, brought Ferguson to his feet in fury.
The next time Ferguson was venting his frustration was at Hernandez, for showboating, by which time Rooney had taken centre stage.
Twelve months ago, the United forward was in the middle of his own personal hell. Now it is as though all that trouble never happened.
He took a leaf out of Hernandez's book when he netted a carbon copy of his strike partner's early effort.
Jones deserved much of the credit for the quick thinking that allowed him to retake possession after finding Nani with a throw, then fizz over a cross that Rooney tucked home.
It was evidence of Jones' intelligence. Minutes later, the teenager was showing off his skills.
Moved into a right-back role Chris Smalling performed so well in last month that it brought him two England caps, Jones began a gallop on halfway that took him weaving into the Bolton area.
Had he found a finish as well, the former Blackburn man would have been celebrating possibly the best goal he would score in his entire career, as well as the first.
Instead, Jussi Jaaskelainen played spoilsport, keeping the ball out with his foot but diverting it straight to Rooney, who stroked into the far corner.
Hernandez had another ruled out for offside before the half-time whistle blew but he wasn't to be denied for long.
After Jaaskelainen had produced an excellent save to deny Anderson, United again laid siege to the Bolton goal and when Michael Carrick's shot was deflected into Hernandez's path, the Mexican wasted no time in belting home.
It was hard not to feel sorry for Bolton, who at times were contributing well. However, they were trying to stop a team of perpetual motion, currently at the top of its game.
And Rooney is now as good as he was bad.
Another Nani cut-back, another unstoppable shot to the corner and the United man had bagged hat-tricks in consecutive games, following Les Ferdinand, Ian Wright and Didier Drogba in achieving that particular feat during the Premier League era.
Rooney almost set Hernandez up for his hat-trick goal and then the Mexican came within inches of providing Anderson with a tap-in.
It was all rather irrelevant given the final scoreline, with both Manchester clubs still to drop a point in what has already turned into a fascinating duel.