The 19-year-old Brazilian needed oxygen on the pitch and was taken straight to hospital for further treatment following a tackle by Emanuel Pogatez.
"He was kept in hospital overnight for observation and to assess whether there was any ligament damage to his knee," United announced on their official website.
Alex Ferguson said he hopes he never sees another tackle like it and even Middlesbrough manager Gareth Southgate admitted he had no complaints at the instant red card shown to Pogatetz during the second half of the match.
"You don't want to see things like that and I hope I never see anything like it again," said the United boss.
"It is such a pity for the boy and took the gloss off what was a really good performance.
"The thing that gets me about challenges like that is that the opponent always claims he has done nothing wrong.
"He [Pogatetz] should have just walked off the field. Then you get their bench screaming that it wasn't a sending off and there is nothing wrong with our player.
"At least Gareth Southgate was very good about it. He apologised and understood the gravity. It was an absolutely terrible tackle."
Southgate branded the challenge "poor" and admitted members of his bench had stepped out of line.
"A couple of lads on our bench did not have the same view as I did but that is dealt with now," he said.
"We can have no complaints about the decision. It is difficult to know why it happened.
"It was an unusual aberration for him because his discipline has improved in the last two years."
Boro never looked the same team after Pogatetz had gone off.
At that point, the Teessiders had levelled through Adam Johnson after Cristiano Ronaldo had marked his first start of the season with his first goal since the Champions League final win over Chelsea in Moscow.
And Ferguson feels the furore involving Real Madrid has is now well and truly behind the 23-year-old.
"I think Cristiano has come to accept that at this stage of his career, United is the place for him," he said.
"Southern Europeans want at some point to play for Real Madrid or Barcelona, so I understood what was going on in Cristiano's mind when he declared he wanted to join Real.
"But once we had talked he accepted it was a move for the future.
"I pointed out to him how much better it would be to leave like Eric Cantona, with the fans loving and appreciating him.
"The crowd still chant Cantona's name and I told Cristiano, 'Leave a hero like Eric' and one day he will. But not yet."
Without Pogatetz, the visitors lost their shape and Ryan Giggs took advantage of Gary O'Neil's slip 11 minutes from time before Nani sealed a place in the fourth round in stoppage time
