Standing over an opponent is usually an attempt by a player to intimidate or threaten, and as such, must be dealt with firmly and quickly by the referee.
Howard Webb (ENG) gives us a textbook example of how this is done.
Note the short, sharp whistle blasts, the quick presence, and then the firm point to the Brazil defender. This was almost certainly accompanied by a firm verbal command to leave the area.
This is one of those “little things” that referees at the top level always seem to get right.