The Super Bowl ended up as another one of those games that happens sometimes in the DVOA system, where the team that's more efficient over the course of the game loses because it groups its inefficient plays into three-and-outs (and in this case, four-and-outs) and thus ends up running fewer plays than the other team.
San Francisco ended the game with 44% DVOA, while Kansas City ended the game with 21% DVOA. This suggests that based on the play in this game, we would expect San Francisco to be the better team in the long run. But of course, the Super Bowl isn't about the long run.