Jones, who was superb in shackling Everton dangerman Marouane Fellaini during Sunday's 2-0 victory, will be central to manager Alex Ferguson's plans for the Bernabeu clash.
However, he limped off early in the second half and Ferguson said they did not yet know the full extent of the problem.
"He got a kick in the calf and we'll have to monitor it," Ferguson told the club's website (www.manutd.com)
Central defender Jonny Evans also had to come off suffering with cramp but should be available for the Madrid match.
"I think he's just lacked a couple of games," Ferguson said.
"He only had 45 minutes for Northern Ireland in midweek. He had to travel to Malta for that. We'll see what he's like (Monday).