Ferguson has endured a remarkable week at Old Trafford and, after finally persuading Wayne Rooney to sign a new five-year contract, saw his side produce a laboured display before winning 2-1 at the Britannia Stadium on Sunday.
Hernandez flicked in a header in the first half but Stoke substitute Tuncay curled in a marvellous equaliser nine minutes from time.
However the Mexican nicknamed 'Chicharito' popped up to poke in a winner with four minutes left to cut Chelsea's lead at the top of the Premier League table to a manageable five points.
Ferguson's teams have made a habit of striking late on throughout his long reign and he admitted that he feared the worst when Tuncay Sanli drew Tony Pulis' side level.
Ferguson said: "When their goal went in, you start to say to yourself it is going to be one of those seasons, but Chicharito came up with the winner.
"The supporters reaction was fantastic to the goal and our players reaction was fantastic. It is the kind of goal United score over the years.
"A late goal met by incredible enthusiasm by the fans. They knew it was an important one.
"Hopefully we can now kick on. We have some important games between now and Christmas time and we have to make our mark in the league now."
Ferguson has been in charge of United for 24 years but can rarely have been in charge through a more turbulent week.
Persuading Rooney to stay may yet prove to be his lasting legacy but he insists the power struggles he has had to contend with come with the turf.
He said: "It is always tough at United.
"There are always issues to deal with. When your top players come towards the end of their contracts you have to do something to get them a new one.
"They are all the same. You have to deal with agents of this world today, which is difficult.
"The players are no problem. There is no problem with players. Some agents are difficult."
Stoke boss Tony Pulis was furious with the decision to not send Gary Neville off and believes that his club are due some luck with referees.
Pulis had already used his programme notes to rail against a lack of decisions going Stoke's way in recent weeks and his mood was not improved when Andre Marriner kept a second yellow card in his pocket when Neville clattered Matthew Etherington three minutes before the break.
Pulis said: "Well let me ask you this, if it was a Stoke City player at Old Trafford and he committed those two fouls, would he have been sent off?
"We've played nine games this season and there have been four decisions which have affected the result.
"We've had three stonewall penalties not given and now this.
"We have been in the Premier League for 85 games now and we've had three penalties so it's a load of rubbish to say that it evens itself out.
"We are very disappointed. We will take it on the chin as we always do at this football club but if the shoe was on the other foot it would have been different.
"I am off to have a glass of wine with Sir Alex now and I doubt very much that he will disagree with me."