Second-half goals from Nani and Javier Hernandez provided enough insurance for United to repel a Reading revival after Jobi McAnuff gave them hope.
But the loss of Jones, who hurt his ankle in the first half after a tackle with McAnuff, is a blow given the England man did such a superb job keeping Real Madrid's Cristiano Ronaldo quiet in the first leg of the UEFA Champions League tie at the Bernabeu last week.
United manager Sir Alex Ferguson admits it is a waiting game but does not expect the 20-year-old to be ready for the Premier League trip to QPR on Saturday.
"We'll have to assess it in the morning," said Ferguson. "It's an ankle injury obviously so I'd imagine he'll not be ready for Saturday anyway.
"But we'll see what he's like after that."