The England international could now be a doubt for the first leg of the Champions League tie against Real Madrid on Wednesday after he limped off in the second half
The former Blackburn Rovers man was replaced after 57 minutes by Michael Carrick after seemingly struggling with a muscular problem for 10 minutes before limped down the tunnel.
Jones had been a doubt before the game after suffering with shingles this week, but appeared to have made a full recovery and started in central midfield.
The England international has had a number of injury problems since joining United, including a back problem which ruled him out from the beginning of the season until late November.
United pulled 12 points clear at the top of the Premier League table following rivals Manchester City's 3-1 defeat against Southampton on Saturday.