Rooney did not start in the 4-3 victory at Old Trafford and manager Sir Alex Ferguson said the striker would miss the rest of the busy holiday fixtures.
"Wayne did it in training yesterday, he could be out for two, three weeks," Ferguson told United's website on Wednesday.
"He did it towards the end of training yesterday. He did it when trying a volley - he strained a ligament behind the knee. It's unfortunate."
United next host West Bromwich Albion on Saturday and then travel to Wigan Athletic on January 1 as they seek to widen their lead at the top of the table, currently seven points.
Rooney's absence failed to blunt United's attack as Mexican Javier Hernandez took his place and scored a 90th minute winner after Newcastle had taken the lead three times.
Robin van Persie was also on target for United, scoring his 13th Premier League goal of the season to move level at the top of the scoring charts with Michu of Swansea City. Rooney has scored seven times in the league this season.
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