Their march towards a record 19th top-flight title was helped by second-placed Arsenal failing to break down Blackburn Rovers in a 0-0 draw at Emirates Stadium that left Gunners manager Arsene Wenger concerned by his side's lack of energy.
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Chelsea's hopes of retaining their title are all but over after being held 1-1 at Stoke City. The Londoners trail the leaders by 11 points in third spot.
Rooney curled in a free-kick midway through the second half before levelling with a low drive. The England striker completed a 14-minute treble by converting a penalty given for Matthew Upson's unlucky handball.
Hernandez added a well-taken goal from close range after being set up by Ryan Giggs and United manager Sir Alex Ferguson said later that his team "played like champions".
Rooney's joy at scoring his first league hat-trick of a below-par season culminated in him having to apologise for swearing on live television while celebrating.
"Emotions were running high and on reflection my heat of the moment reaction was inappropriate," he told the club's website after chalking up 101 league goals for United.
One thing running high at Emirates Stadium was Arsenal midfielder Samir Nasri's huge bump on his head which bulged through his bandage when he opted to play on in the second period following a first-half clash of heads.
Arsenal's best chance came late on when a Nicklas Bendtner shot was blocked on the line and they could not make the most of Steven N'Zonzi's 76th-minute sending off for a two-footed challenge as relegation-threatened Blackburn held firm.
"Overall it was a flat performance with a lack of energy level, lack of sharpness, and it's quite a big concern to see what we have seen today," Wenger told a news conference.
"Very few players looked to have the resources to pick the pace up in the game... before we speak about the title we have to focus on our performance level because it was not good enough today."
