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 Champions League tie at the Bernabeu last week.
"We'll have to assess it on Tuesday morning," said United manager Sir Alex 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."