The 21-year-old has struggled with fitness concerns this season, including ankle damage in September and hip and groin injuries during November.
Jones has, however, started and finished United's last seven games in all competitions, but David Moyes has revealed he will now miss the next two weeks after damaging his knee in training.
Jones had been used in midfield of late, with Moyes struggling with injuries elsewhere in his squad, but the club have been boosted by the return of Michael Carrick and long-term absentee Darren Fletcher.
We can confirm Phil Jones has suffered a knee injury and is expected to be out for a couple of weeks. #mufc— Manchester United (@ManUtd) December 26, 2013