The Mexican goal-poacher, looking suspiciously offside, tucked in the winner in the 75th minute to kill off a vibrant Chelsea side who had battled back from 2-0 down before having Branislav Ivanovic and Fernando Torres sent off by referee Mark Clattenburg in the final half-hour.
Torres's dismissal, for diving, led to a furious touchline row between Chelsea manager Roberto Di Matteo and his United counterpart Sir Alex Ferguson who later said the Spaniard had deserved to go despite replays suggesting he was fouled.
Clattenburg was later the subject of a complaint by Chelsea over "inappropriate language" towards two players.
Chelsea roared back with Juan Mata's free-kick and a Ramires header either side of the interval and United were on the ropes until Serbian right back Ivanovic was sent off just past the hour mark for bringing down Ashley Young.
With the home crowd howling its disapproval and tempers fraying on the touchline, Hernandez - on as a substitute for Tom Cleverley - tapped in Rafael's fierce cross while standing almost on the goal-line.
United's first win at Chelsea for 10 years lifted them back above neighbours Manchester City into second place on goal difference with 21 points, one point behind Chelsea who had ample reason to feel hard done by.
"We must be disappointed that key decisions were wrong," Di Matteo told reporters.
"At 2-2 we looked like the team that was going to win the game. It was a good game between good teams and the official ruined it. Key decisions have to be right and you don't want the referees to have such a big influence."
"The decision the referee has to make is whether the striker has chosen to go down," he told Sky Sports. "He was through on goal - I don't know why he has gone down.
"I think it's his own fault. We've never got breaks down here and had some terrible decisions against us in the last few years. But today we have got a little break for the goal - Chicharito may have been offside."
The Uruguayan celebrated with a theatrical dive in front of Everton boss David Moyes, who had been critical of Suarez's habit of going to ground in the build-up to the game.
