The England defender has played just 18 times in the 11 months since his £8million move from Leeds United, and now looks set for another spell on the sidelines.
"He'll have the scan on Monday, and until we get the results we won't know how long he'll be missing for," Sir Bobby told club's official website.
"It's not a recurrence of one of his old injuries, it's a brand new injury but like I say we won't know the seriousness of it until Monday.
“It’s a shame and it’s the only disappointment to come from what was otherwise a good day for us.
“Ironically he’d been playing the best he had since he came back from his two-month absence.”
If Woodgate is ruled out of the trip to Charlton it’ll mean recalls for Andy O’Brien and Steve Caldwell, with Titus Bramble banned after collecting five cautions and Andy Griffin’s suspension for his sending off in the reserves leaving Aaron Hughes unable to move into the middle.
Craig Bellamy and Lee Bowyer will also miss the game because of injury.