"If this was not a major championship, I think he probably would have to go home right now after this round."

Before Tiger Woods hit his second shot on the 18th hole, Johnny Miller made this comment about the pain he's going through:

You see a lot of deep breathing by him that he is really having to pull it all together. And if this was not a major championship, I think he probably would have to go home right now after this round. I really believe that. 

The most likely scenario is that Woods has irritated the inflammation that is already in the joint.  That can cause swelling, and icing it should help.

One of the big question marks following the U.S. Open will be whether or not the knee is healthy enough to go another 72 at Congressional in three weeks.