Hernandez was hurt heading a ball awkwardly during training at the Red Bull Arena in Harrison, New Jersey.
He is now expected to miss the Community Shield in 10 days' time, and faces a race to be fit for their opening Barclays Premier League match at West Bromwich.
Sir Alex Ferguson confirmed that the Mexico international fell ill after heading the ball awkwardly 'on the top of his head' in training on Tuesday night.
Time off: Hernandez only recently joined United's tour of America after playing for Mexico at the Gold Cup
Doctors initially favoured keeping Hernandez in for observation until Friday but agreed to let him leave onWednesday after seeing the results of scans.
Hernandez rested at the team hotel while United beat the Major League Soccer All-Stars 4-0 at Red Bull Arena and has been cleared to travel when they fly to Washington DC on Thursday ahead of their final tour game against Barcelona.
He will not be allowed to play for a fortnight, although Ferguson doubted whether Hernandez would have featured in that time anyway as he is eased back to fitness after a longseason which ended with Mexico's participation in the Gold Cup and a brief holiday.
'He is back in the hotel,' said Ferguson, after United beat the All-Stars. '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's okay for that. He got concussion in training and we dealt with that. We took him to hospital, he had a scan, it was all clear.'
Fast start: Javier Hernandez made an instant impression for Manchester United with an excellent debut season
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.'
Pleased to see you: Wayne Rooney greets David Beckham in New Jersey
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.'
While Beckham returns to his day job with LA Galaxy, United will head to Washington on Friday 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.'
MLS All-Stars 0 Manchester United 4: Berba outshines Becks as United romp in USLittle Pea KO drama: Concussed Javier Hernandez goes to hospital after heading ballSign up for our FREE Fantasy Football game and your chance to win a share of ?40,000All the latest Manchester United news, features and opinion