While Majora has evidently the better mind and fighting style he just can't touch Zant.
However if think about confrontations in other ways, say by being tricked by the other into servitude it'd be simple to guess who'd win.
By the way, is this one on one? Like with nobody lending power from the shadows? In that case, Majora.

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Memories of the world
before the fall remain...
But the light of dawn doth never change,
nor e'er the hearts of men...