The Mexico striker scored in the 75th minute to inflict the league leaders' first loss of the season and put United just a point behind Chelsea.
``It was a really difficult game as they commanded at the end of the first half, we were very lucky we scored the last goal,'' Hernandez said. ``For some people it will be very controversial, for others it won't. For us, we won the three points and it was very difficult.''
United threw away a two-goal lead established inside 12 minutes. Robin van Persie saw his shot turned in by Chelsea defender David Luiz before getting on the scoresheet himself.
Chelsea fought back as Juan Mata curled in a free kick just before half time and Ramires headed in an equalizer eight minutes after the break.
Chelsea defender Branislav Ivanovic was sent off in the 63rd for bringing down Ashley Young, and striker Fernando Torres received a second booking for diving.
``It's a shame a game like this has to be decided in this manner by officials,'' Chelsea manager Roberto di Matteo said. ``Surely when he watches the images he (the referee) will realize he made a big mistake.''
Chelsea had not lost at Stamford Bridge in a league match to United since Roman Abramovich bought the club in 2003, and he watched in frustration as his side's comeback counted for nothing.
``It's been 10 years since we have won down here,'' United manager Alex Ferguson said. ``We had a good record until Jose (Mourinho) came along (in 2004) and spoiled the party.''
Chelsea will have a chance for revenge on Wednesday when the teams meet again in the League Cup here.
Early on, Chelsea appeared to be missing captain John Terry, who was serving the second game of his four-match ban for racially abusing an opponent.
After just four minutes, United ripped through Chelsea's defense down the right with Young laying the ball off to Wayne Rooney, who squared to Van Persie in the penalty area.
The Netherlands striker's shot came off the post but it bounced off Luiz into the net.
Chelsea's brittle back line was sliced through again in the 12th when Rafael da Silva was given too much space to storm down the right flank unchallenged.
The defender slipped the ball through to Antonio Valencia, who crossed to the unmarked Van Persie to sweep in his ninth United goal since arriving in August.
United was playing with confidence, pinging the ball across the turf with ease and precession.
Chelsea took time to assert itself on the visitors, but kept United goalkeeper David de Gea busy for the rest of the half, blocking a free kick of Luiz with his outstretched right foot and then thwarting Gary Cahill's header.
But the pressure paid off for Chelsea a minute before the break, with Mata superbly curling the free kick inside the post after Eden Hazard was brought down by Rooney.
The momentum was with Chelsea - and continued after the break as United's defense was the one to be exposed.
The equalizer came eight minutes into the second half as United failed to close down Chelsea's fluid attacking play.
Mata took the ball to the byline and found space to whip in a cross that Torres headed across to Oscar. The Brazilian then chipped across to Ramires, who rose above Tom Cleverley to head past De Gea.
As the hosts continued to pressure the United defense, their plan was ripped apart by being reduced to 10 men in the 63rd when Ivanovic brought down Young, halting his advance to goal.
Six minutes later, referee Mark Clattenburg pulled out the red card again to further infuriate Chelsea.
Having been booked at the end of the first half for a foul on Cleverley, Torres received a second yellow card after being adjudged to have gone down too easily under Evans' challenge.
``I made a bit of contact but I don't feel it was enough to bring him down,'' Evans said. ``I think he probably realized he wasn't getting the ball and went down.''
Hernandez restored United's lead in the 75th, 10 minutes after replacing Cleverley.
Van Persie's initial shot appeared to be creeping into the bottom right of the net after Cech got a touch to it but the goalkeeper hacked the ball away.
It fell to Rafael, whose shot was turned into the net by Hernandez, although the striker later accepted he might have been offside.
Just after Hernandez's winner, a steward in front of Chelsea fans fell to the ground and was still receiving treatment as the match ended.
``He slipped and fell and may have hurt his knee,'' Chelsea spokesman Steve Atkins said, refuting initial suggestions that the steward was hit by an object.
Courtesy of ScoreMobile (http://m.thescore.com/scoremobile)
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