Selected at right-back, Jones was hurt after attempting to tackle Reading captain Jobi McAnuff and it was immediately obvious the former Blackburn Rovers man was in considerable pain. Jones headed straight down the tunnel and it seems the man who helped subdue Cristiano Ronaldo in the first leg of United's Champions League last-16 tie with Real Madrid at the Bernabeu faces a battle to be fit for the return on March 5.
The injury took the gloss off a victory that keeps United on track for a repeat of their historic 1999 treble, and Sir Alex Ferguson on course for a possible encounter with Rafael Benitez, whose Chelsea team must beat Middlesbrough for the right to face the Old Trafford side in the last eight.
The third goal of Nani's largely disappointing season and Javier Hernandez's 15th strike of the campaign took the hosts through, although McAnuff's late effort ensured United were never able to relax.
"Everyone is ready to help the team," the 26-year-old Nani said. "I was glad to get an opportunity to come on [to replace Jones], I enjoyed the game and helped the team. I scored the first goal and that changed the game and I am pleased to get an assist to help the team to this big win."
Hernandez took his tally for the season to 15 and acknowledged how tough opponents Reading had been.
"We know they are difficult, they wanted to score for the draw but we are very happy to go through," said the Mexican.
"Then Nani came on, got the first goal and he was brilliant and made chances for us. We were respectful of them, they are a very good team and we`re very happy. Now we have to focus on QPR in our next game."
Manager Sir Alex Ferguson hailed his side for their all-round performance. "It was a good cup tie and ended up a really good one," he said.
"They [Reading] went for it, piled the ball into the box and we withstood that. We played some great football, missed chances, had shots blocked and their goalkeeper made some saves.
"I'm satisfied with the quality of the game. We had to defend, our goalkeeper made some excellent saves because at 2-0 we were never comfortable."