Jones was forced off with a knock in Sunday's win over Everton but was on the plane that flew to the Spanish capital.
Ashley Young and Jonny Evans also travelled, along with Anders Lindegaard, meaning Sir Alex Ferguson's squad will be almost at full strength for their trip to Spain.
It has been predicted Jones will be handed a midfield holding role, after successfully shackling Gareth Bale and Marouane Fellaini in recent weeks. Ferguson has alternatives though, which include Tom Cleverley and Anderson, even though Michael Carrick is among those virtually certain to start.
Scholes did not make the trip as he has been suffering with a knee problem.
For Madrid, former Liverpool midfielder Xabi Alonso is expected to be fit and did train despite doubts being expressed in the Spanish media about his participation. Local reports also suggest up to 5,000 United fans will fly in for the game, a significant number of them without tickets.
Evans does not feel United have any reason to feel inferior against Madrid, who are 33 matches undefeated on home soil since they were beaten by Barcelona in 2012 and in four meetings with United at one of world football's citadels the worst they have done is draw twice.
However, Evans does not view that as an excuse to fret. After all, United are now within touching distance of a record 20th league title and their record of three Champions League finals in the last five seasons far exceeds Real's record over the same period, which includes just two semi-final appearances.
"We can't be daunted," said the Northern Ireland defender. "We are Manchester United. Teams look up to us as well.
"I am sure the same pressures will be on them. They have good players who can hurt you but we play against Premier League opposition every week and that is one of the best leagues in the world. It is just as if we were playing against Manchester City or Liverpool. They are top players and we have to be spot on."