The Football Association today launched a formal investigation into allegations Mark Clattenburg used “inappropriate language” towards John Obi Mikel and Juan Mata during Chelsea's acrimonious defeat to Manchester United.
Hernandez struck 15 minutes from time to help United claim their first top-flight win at Stamford Bridge in over 10 years.
The victory extended United's winning streak to five matches and also narrowed the gap on league leaders Chelsea to just one point.
United's defensive frailties, and Chelsea's devastating early-season form, had led many to claim the Blues are better equipped to win the league this season than their Lancashire rivals.
So having helped his team stifle Chelsea's comeback with his second-half winner, Hernandez was under no illusions as to how important the three points were to his club.
"This game could have changed the title," the Mexican said.
"That's why it was important we didn't allow them to get ahead.
"It was vital to get the three points at a very tough place. We are in there in the fight to win (the Premier League)."
After a slow start, United have started showing signs they are back to their best.
Ferguson's team have racked up wins against old rivals Chelsea and Liverpool, and midfielder Michael Carrick believes the team must continue their good record against the top sides when they host Arsenal next weekend.
"It's important to take points off your rivals likes Liverpool, Chelsea and Arsenal next week," he said.
"Next week is just as important. It's a good start to the season.
"We've obviously had a couple of defeats but we've bounced back and we're still in a good position, so we can be happy."
Yesterday's game lived up to its blockbuster billing, with five goals, two red cards and a series of contentious refereeing decisions that sparked a furious row between Ferguson and the Chelsea bench on more than one occasion.
Then it later emerged that Chelsea had made an official complaint to the Premier League alleging that referee Mark Clattenburg had used "inappropriate language" toward two of their players. The referee later said he would co-operate fully with any investigation.
Clattenburg's decision making, and that of his assistants, proved to be the main talking point directly after the match, however.
Clattenburg issued Fernando Torres with a second yellow card for simulation when he was clipped by Jonny Evans, and the referee's assistant also failed to notice that Hernandez came from an offside position to turn home Rafael's cross for the winner.
Being a striker, Hernandez was not too bothered about being in an offside position when he scored.
"I don't' care... the referee counted it," the 24-year-old said.
"When Robin (van Persie) shot and (Petr) Cech made a great save I went for the rebound and the ball went to Rafael.
"The first thing was to get along the line of defenders because I thought that was where the ball was going to go. Thankfully I reacted well to it."
The Mexican did show his selfless side, though, by playing down the importance of his contribution to the win.
"It doesn't matter who scores the goals," said the Mexico striker, who has scored three goals in his last two games for United.
"It has been a good week for me. But the most important thing for me is to have the minutes on the pitch and help the team."
Ferguson was impressed by Hernandez's killer cameo which may have earned him a place in United's starting XI for Wednesday's Capital One Cup clash at Chelsea.
"He's brilliant in there and he took a lot of punishment, too, there were a lot of tackles against him," Ferguson said.
"But he's such a courageous little lad, such a tough cookie.
"He's always going to be a threat to defenders and he's got the winning goal in an important game."