The champions took an early lead when Hernandez pounced at the near post.
Rooney converted Phil Jones' cross to make it two, then the England striker profited from another of the defender's runs to add a third.
Hernandez swept in a fourth before Rooney drilled in his third - but Tom Cleverley may have broken his foot.
Crumpling under a heavy challenge from Kevin Davies, the midfielder was replaced midway through the first half.
But it was the only blemish for Sir Alex Ferguson's side after another impeccable performance brought up their 200th away win in the Premier League - the first club to achieve the milestone.
United's last trip to the Reebok Stadium ended in a 2-2 draw almost a year ago, when they had to rely on a late Michael Owen header to salvage a point.
But this encounter was very different as Hernandez, making his first start of the season, gave United the perfect opening.
Showing the superb movement he is renowned for, the Mexico striker lost Gary Cahill with a darting run to the near post to steer in Nani's tantalising low cross from the right.
The goal came while United were temporarily down to 10 men following the injury to Cleverley.
Bolton looked to hit back immediately, but former United midfielder Chris Eagles saw his shot cleared off the line by Rooney.
Despite the high-profile errorsUnited's new goalkeeper David De Gea has made this season, he went some way to silencing his doubters with an impressive flying save from Ivan Klasnic's long-range effort. And the stop ignited United, who made it 2-0 just 74 seconds later.
United's verve and invention overwhelmed Bolton and Rooney doubled United's lead in the 20th minute.
Catching the home side napping, Jones whipped in a devilish cross from the right to Rooney, who found himself between Cahill and Dedryck Boyata before prodding in from close range.
Rooney poured further misery on the home side, making it 3-0 in the 24th minute with a goal engineered by Jones, whose stature is growing with every game.
Exploiting a gaping hole in the home side's defence, Jones' twinkle-toed run took him into the penalty area, before he squared the ball to Rooney to find the back of the net with the easiest of finishes.
With manager Owen Coyle barking instructions from the touchline, Bolton limited United to three in the first half but, while Klasnic and Martin Petrov linked well at times, the home side were painfully short of creativity.
It was only a matter of time before United added to their lead and, two minutes before the hour mark, Hernandez made it 4-0.
Substitute Michael Carrick found the Mexican lurking at the far post and, with the Bolton defence at sea, his low effort had Jussi Jaaskelainen well beaten.
Nigel Reo-Coker struck the crossbar as Bolton desperately looked for a route back into the game but, minutes later, Rooney put the gloss on the win with United's fifth - and his third.
Collecting Nani's cut-back from the right the England striker nonchalantly struck his hat-trick goal from the edge of the box to give him his seventh career treble.
Rooney also becomes the fourth player to score back-to-back Premier League hat-tricks after Les Ferdinand, Ian Wright and Didier Drogba.
Sequels rarely match the original and United's short trip to the Reebok was always likely to pale in comparison to their famous 8-2 mauling of Arsenal a fortnight ago - but United remain the team to beat after another scintillating display.
bbc