Naruto only won because of the plot.
Naruto had such difficulty fighting Pain and then Nagato again for using the Rinnegan:
And Sasuke didn't just have the rinnegan but serious intellect.
They were both given upgrades by Hagoroomo so they should have equal strenght in that sense, but Naruto fighting someone with the Rinnegan and that knows how to use it, he should have lost. Sasuke is better than him.
Naruto had such difficulty fighting Pain and then Nagato again for using the Rinnegan:
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And Sasuke didn't just have the rinnegan but serious intellect.
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They were both given upgrades by Hagoroomo so they should have equal strenght in that sense, but Naruto fighting someone with the Rinnegan and that knows how to use it, he should have lost. Sasuke is better than him.