Second-half goals from Nani and Javier Hernandez provided enough for United to repel a Reading revival after Jobi McAnuff gave them hope. But the loss of Jones, who hurt his ankle after a first-half clash with McAnuff, is a blow given he did such a superb job keeping Real Madrid's Cristiano Ronaldo quiet in the first leg of the Champions League tie at Real Madrid last week.
"We'll have to assess it in the 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."
Saturday's trip to QPR is the least of Ferguson's worries, though, with the obvious requirement now for Jones to be patched up for that Real rematch at Old Trafford on March 5, which will now be followed by an FA Cup quarter-final against either Chelsea or Middlesbrough.
And Ferguson might even have an unexpected selection dilemma given Nani's introduction for Jones sparked United into life after they had faded following a decent opening. And Ferguson sensed he might have a big impact against Reading.
"He's got great talent, we know that," said Ferguson. "I had a feeling he would win the game for us. You could see he was right on form the moment he came on.
"He had two great strikes immediately and was a threat to them the whole night. It's a good addition. If he keeps that form it makes my job more difficult now."
Nani's opener broke some stubborn Reading resistance, which threatened to earn them a replay. Hernandez seemed to take the game away from them completely with his 15th goal of the season shortly afterwards, only for McAnuff to pull one back which ensured a few nervy moments at the end before United were able to take another stride forward in their Treble quest.
"The last 10 minutes were a bit scary," said Ferguson. "Some of the football tonight was fantastic and we could have scored a lot of goals. In that way I'm satisfied.
"We didn't want a replay though and in fairness, we dug in and defended the long throw-ins and the balls into the box. You cannot get any better than a home tie in the cup. It doesn't matter who we play, at Old Trafford we have got a chance."