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Austrian Andreas Weimann had stunned United with two well-taken goals for lowly Villa either side of the break but Mexico striker Hernandez showed his killer instincts by netting on 58 minutes and seeing a second shot deflect in off Ron Vlaar.
The livewire forward sealed the remarkable comeback with a diving header three minutes from time.
United stretched their advantage to four points after 11 games ahead of second-placed Chelsea and Manchester City who host Liverpool and Tottenham Hotspur respectively on Sunday.
Arsenal's topsy-turvy season took another turn for the worse when they let slip a two-goal lead and missed a late penalty to draw 3-3 at home to a Dimitar Berbatov-inspired Fulham.
Olivier Giroud's double - his first home Premier League goals - could not prevent Arsenal staying seventh in the table, sliding four points behind fourth-placed Everton who came from behind to beat visiting Sunderland 2-1.
Surprise packages West Bromwich Albion, in fifth, are level on points with Everton following a 2-1 victory at Wigan Athletic thanks to James Morrison's header and a Gary Caldwell own goal.