Hernandez was forced off due to injury in the second half of United's fifth straight win of the season after being on the wrong end of what Ferguson felt was a "shocking tackle" from the England full-back.
It is not known how long the Mexican will be sidelined for.
However, Hernandez was in obvious pain as he hobbled down the tunnel and Ferguson was not impressed.
"It was a shocking tackle," he told MUTV.
"The referee booked him, so I don't understand why he hasn't given a penalty.
"Ashley Cole is very reckless at times. He is committed of course but being committed you can sometimes go over the edge a bit.
"That was an example of that."
Even Chelsea boss Andre Villas-Boas admitted it was not the greatest tackle.
However, Villas-Boas felt the incident might not have happened if the officials had got two earlier offside decisions correct, which would have wiped out goals for Chris Smalling and man-of-the-match Nani.
"Maybe he wouldn't get sent off if the linesman does his work," said Villas-Boas. "He [Cole] would have been less emotionally drained.
"I work the other way round. You are trying to say the referee did something wrong. I cannot forget the previous two.
"If it was 0-0 maybe Ashley is a little bit more mentally in control of the situation and doesn't do the red card foul that you mention."
Phil Dowd's decision to book Cole means that the matter is now dealt with, although television replays indicated the Chelsea man had been lucky to escape with only that sanction.
However, Fernando Torres will not be wanting to watch the game again after he followed up his second goal for the Blues with an embarrassing miss after rounding David de Gea but firing wide of an empty net nine minutes from the end.
Ferguson diplomatically labelled it "a bad miss". Villas-Boas was even more sympathetic.
"You have to be fair," he said.
"Today two of the best strikers in the world missed crazy chances.
"It happened to Fernando and Rooney. It is nothing dramatic. Sometimes the ball goes in. It didn't fall our side.
"Normally it is 3-2. At that point it might have given us a mental edge for the last 10 minutes.
"We would have been completely exposed at the back but we would have taken the risk to try and get a draw. It didn't happen."
Villas-Boas was referring to Rooney's 'Moscow moment' when, in an incident just like the one John Terry suffered to cost his side victory in the 2008 Champions League final, the United striker slipped as he went to take a second-half penalty.
In addition, Ramires and Dimitar Berbatov when it seemed like it was easier to score, although in both instances, Ferguson felt the players had been let down by the passes.
"Both passes were terrible; Torres to Ramires and Wayne's to Berbatov," said Ferguson.
"It was very difficult to get proper connection on them because the ball's going all over the place."
Chelsea had 24 shots, a staggering number at Old Trafford.
However, they were out of the game by the interval as Rooney's ninth of the season followed earlier efforts from Smalling, who later suffered a groin injury, and Nani, when Chelsea's defences looked alarmingly weak.
It completed United's best start to the season since 1985 and equalled a club record 18-match winning sequence at home.
"There were so many mistakes in the match from both teams," said Ferguson.
"We have won a game where we were so careless. We could have thrown it away."
It was Villas-Boas' first defeat as Chelsea boss, which leaves his side five points adrift of the hosts, who are now two points clear following Manchester City's failure to hold onto a two-goal lead at Fulham.
"As I said before, nothing that happened here would mean anything in the Premier League table," said Villas-Boas.
"It is an [unpredictable] league.
"Manchester City have the most amazing squad as well, but they didn't win. Arsenal and Liverpool lost.
"All of the five contenders are there. Anything can happen.
"The most regular is United at the moment but we showed we are up to the level of the champions.
"This game didn't go our way. But we will be up there competing for the title, I am glad Sir Alex corroborates."