The Seahawks ran a route-jumping scheme in the secondary. Basically, for example, KamChancellor would recognize the crossing route, peel off his man further down the field (while Earl Thomas then picked up that receiver), and Chancellor (or whoever peeled of the downfield receiver) would be there to stop any YAC. You have to have a very intelligent secondary to run this scheme, though, because if even on of the nickelback or safeties doesn't read the peel, then Denver would have a wide open receiver running down the field.
The pass rush made it possible for this peel, too. It was a masterpiece in a 'bend but don't break' defense. Early in the game when Chancellor blew up Thomas on a crossing route, it was over for Denver. YAC is how Denver moves the ball, and Quinn's scheme made that all but impossible.
Also, LOL at the 49er fan who says the 49ers were a better team than Seattle. That's just the whining of the fans of a losing team.