I have thought about this issue for a few hours now...
Superman obviously has the strength and physical advantage, but Batman is smarter, and since Lex Luthor has put Superman in danger so many times, Batman could do so as well with the use of some well placed kryptonite.
As both are naturally 'good' deep down, each would not want to kill the other, and I think that capturing and confining Batman and thus 'defeating him' would be easier for Superman to do than the other way around(hell, even Ceasar Romero and Eartha Kitt were able to capture Batman!).
Although I am a bigger Batman fan, I would have to give the edge to Superman, BUT... that is only if one does not consider the all important "Robin factor".