Nadal did. That was an incredible match, wasn't it? Fortunately, the H2H doesn't show just the winner of the last match, but sums up the entire rivalry, whether it's overall or on each surface. 2 wins and one loss on grass is a positive H2H, regardless of the order. Same thing goes for HC (6-5). I'm not saying that Nadal is ahead between them for no reason, but while Federer has been making it to almost every RG final (along with other clay events) and falling short only against the king of clay (most of he time), Nadal hasn't been good enough to earn the right to face Fed that often on faster surfaces.
Oh? So Rafa has beaten Roger 6 times on non clay surfaces whilst Roger has only beaten him twice on clay ? Interesting.