Hernandez spent Wednesday evening in his hotel room in New Jersey after being released from hospital after being admitted following training 24 hours earlier.
Although medical staff found no major damage, Ferguson has confirmed the Mexico forward will not play for a couple of weeks, even though he will continue to train and remain on tour.
"He got concussion in training and we dealt with that," said Sir Alex Ferguson.
"We took him to hospital, he had a scan, it was all clear.
"He is back in the hotel. He is in his room and will be out for a couple of weeks.
"He would never have been available for Barcelona anyway because he has just come back from his break after the Gold Cup.
"He will travel with us though. He is okay for that."
In Hernandez's absence, Dimitar Berbatov took the opportunity to shine, helping to create United's excellent opener before smashing home the third right after half-time.
Both fulfilled the Bulgarian's preferred criteria of 'beautiful goals' and helped break his duck for the tour.
In between, Park Ji-sung scored a fine goal to maintain his impressive recent form.
The South Korean then indicated he would be willing to sign the two-year contract extension Ferguson confirmed in Seattle last week had been offered.
"Why not?" said the midfielder
"I keep saying I want to stay here for more years to win things with Manchester United.
"Hopefully one day we will get together."
United's fourth straight victory on their five-match tour was completed by Danny Welbeck, to leave David Beckham empty-handed against his former club.
"When you don't put chances away against a team like Manchester United, they will capitalise," said the ex-England skipper.
"I had many successful years playing under Sir Alex Ferguson. I wouldn't be where I am today without him.
"He gave me a chance when I was 16. I owe him a lot. To play against a team that is still managed by him is emotional."
Whilst Beckham returns to his day job with LA Galaxy, United will head to Washington on Thursday for a meeting with the team that clinically defeated them at Wembley in May.
"It is only pre-season," cautioned Ferguson.
"I just want the players to go out and enjoy it."