The Mexican had come closer than any other United player to breaking the stubborn resistance of an Everton side who could have had a couple of penalties and for whom goalkeeper Tim Howard was outstanding.
But additional heroic performances from Phil Jagielka and Sylvain Distin counted for nothing as Hernandez rose to meet Antonio Valencia's far-post cross.
The striker powered in his 19th goal of a sensational debut campaign to send United into the Champions League semi-final with Schalke in winning mood and knowing if they can avoid defeat to Arsenal and Chelsea in their next two league games, they will surely knock Liverpool off the perch they have occupied for so long.
Jonny Evans was fortunate referee Peter Walton did not view his tackle on Jermaine Beckford as a foul midway through the opening period, and how Rio Ferdinand got away with shoving substitute Victor Anichebe over when the Everton man had outpaced him in a race towards the United goal was difficult to fathom.
Everton's luck was also out when Jack Rodwell let fly from the edge of the area with a shot that took a deflection off Evans and was heading for the bottom corner until Edwin van der Sar got the slightest touch.
Source: PA
Source: PA