Monye was taken to hospital after being knocked unconscious in a tackle in the first half of the 57-31 tour win at Profert Olen Park.
The 29-year-old Harlequins back, playing his first match of the tour after a hamstring injury, received prolonged attention on the field before being carried off on a stretcher but Lancaster delivered a positive report.
Head coach Lancaster said: "Ugo was knocked out during the tackle. He was taken to hospital but he has come round and he is fine, albeit a bit groggy.
"I have only just had medical updates but I think he will be travelling back with us.
"He will go through the concussion protocols and he will struggle to be fit for Saturday."
England were due to travel back to Johannesburg before heading to Port Elizabeth for Saturday's third Test against South Africa.
The tourists are hoping to gain a consolation win after defeats in the first two matches of the series.
The odds will still be against them but they will at least head south upbeat after a hard-fought win for the second string in Potchefstroom.
Nick Abendanon claimed a hat-trick of tries while Monye's replacement Jonny May, a late call-up to the squad, touched down twice. There were also tries for Ben Morgan and Anthony Allen as well as a penalty try.
The Barbarians scored four tries themselves and tested the tourists in the second half when Jamie Gibson was sin-binned.
Lancaster said: "There are lots of positives we can take positives from the performance although there were one or two areas where we let it slip, particularly in that third quarter defensively.
"I think it was important to put in a positive performance.
"We wanted to improve on the quality of the performance we put in last week. I thought there was a better intensity and shape about what we did.
"I thought the boys adapted to the conditions better, and they have been here a week now. It was good for the boys in the stand watching as well."
Captain George Robson now hopes the Test team can maintain the momentum to wrap up the tour on a positive note.
The Harlequins forward said: "On the morale and the win, I think it is massive.
"We can take a lot from it and a lot of the younger guys have come through it.
"It was a bit hairy out there and it could have gone one of two ways when we had a man in the sinbin.
"I think the younger guys will have learned a lot from that, in sticking to our approach, backing things up and turning things around again.
"It is great to get the win. We said we wanted to get the win and help build the momentum going into the last week, finishing the season on a high."
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