Wayne Rooney was persuaded this week that Sir Alex Ferguson's men remain the team to beat, but an extraordinary few days at Old Trafford looked set for a miserable finish when Stoke substitute Tuncay hit a sublime 82nd-minute equaliser to cancel out Hernandez's first-half header at the Britannia Stadium on Sunday.
However, summer acquisition Hernandez found time to sweep in a late winner which closed the gap on leaders Chelsea to five points.
Central to Rooney's push for a move away was a claim that the club, burdened with debt ever since the Glazer family's takeover, could no longer match his ambition by attracting the world's top players.
While that may be true to some extent, Hernandez is looking a more astute purchase by the game as he notched his fourth and fifth goals since joining from Guadalajara for around £7million over the summer.
Facing away from goal, the little Mexican still managed to open the scoring in the 27th minute with the back of his head in what was a fine piece of finishing.
Gary Neville was then incredibly fortunate not to be sent off at the end of the first half when referee Andre Marriner declined to show him a second yellow card for a rash challenge on Matthew Etherington.
Stoke boss Tony Pulis will be understandably furious with the decision, but the fact remains that despite dictating play for large periods the Potters were unable to test Edwin van der Sar once until Tuncay's fine strike.
And that lack of cutting edge proved crucial when Hernandez reacted quickly to poke in the winner with four minutes left.
The home side had enjoyed a spell of pressure before United forged ahead through Hernandez.
Nani worked a short corner with Patrice Evra and when Nemanja Vidic headed the ball back across the face of goal, the Mexican international was able to flick home his header despite facing away from goal.
Stoke responded well as they again dictated play and Neville became the first name in referee Andre Marriner's book for a clumsy challenge on Matthew Etherington.
Neville was then extremely lucky not to see red after another mistimed challenge on Etherington.
Neville surprisingly reappeared with the rest of United's players at the break but was then humiliatingly instantly replaced by Wes Brown before the half could kick-off.
Pulis introduced Tuncay and Eidur Gudjohnsen in a bid to add more quality in the final third and the two combined in an 82nd-minute equaliser.
Paul Scholes gave the ball away and after Kenwyne Jones and Gudjohnsen linked up, Marc Wilson swept a fabulous pass out wide to the Turk.
Tuncay cut inside onto his left foot to sweep a stunning finish over the head of Van der Sar and into the top corner.
It was the first goal Stoke had managed past United since Mark Stein's double in a League Cup tie in 1993 and was well worth the wait.
Ferguson's men could write the book on late goals, however, and Hernandez was again the crucial man as he poked in Evra's mis-hit shot from five yards with just four minutes left.