Naruto didn't lose their taijutsu battle. It was a tie.
When their taijutsu battle started Naruto wasn't using any mode (body power), but Sasuke was using his sharingan (eye power). Yes, I know Naruto was using his shadow clone -
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Sasuke continued to use the sharingan after Naruto's clone vanished -
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Yet, Naruto was still able to get a solid hit on Sasuke with no clones -
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Then Sasuke sharingan vanished and from that point they were evenly matched in taijutsu -
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PS: I wished we could have saw them fight in taijutsu when they were still in good condition and I was hoping we would see some frog fu, but I don't thing that is going to happen.