First thing you need to know: Any rules that are anything other than the hand rankings (flush beats a straight etc) are subject to be differernt every single place you play. Make sure you understand the rules in any game (home game or card room) before you sit down.
That being said, it's pretty standard that the button pays the small blind when it comes down to heads up in a tourney. The logic behind this practice is that it gives the non-button player a little bit of protection by giving him position for the first betting round. Otherwise the button would have a very dominant posisition for the whole hand, acting last on every betting round.
I've never played in an "organized" tourney that didn't implement the blinds this way when it got down to heads up.