They don't actually have rules officials that walk with every group at The Masters, so it's very likely that no official saw the original drop. They were alerted to a possible rules breach while Tiger was playing 18, they reviewed it and saw no transgression, so no additional penalty. When they were notified of Woods' comments after the round, they had already missed the opportunity for a DQ. A 2 stroke penalty was their only form of recourse. The only way Eldrick wasn't going to play the weekend was if Withdrew himself.
This whole thing was incredibly unfortunate for Woods. His ball had no right to go in the water in the first place. It glanced the flagstick and spun violently backwards. If he makes birdie there, which was very likely, he makes 4 on that hole instead of the eventual 8. He then finishes at 9 under in a tie for the lead.