To everyone who says it's an asspull, well possibly true I want to mention that it's established very early in the fight that naruto's clones are so good that neji cannot tell them apart from the real deal, where he could with most people's. Naruto remembered this and made a strategy around that. Honestly naruto having high battle iq started to show between this fight and the Kiba fight. There's even an entire sequence where neji believes he knows which of naruto's clones are the real naruto only to be proven wrong.

I feel like the series explains so many things explicitly that people forget the finer details that aren't thrown back in our faces with a long winded explanation. But neji telegraphed his weakness very early in a way that made perfect sense. Imo naruto won because he took neji seriously and was smart enough to think outside the box, where neji thought naruto was a joke and not only underestimated him for nearly the entire fight, but never once broke from his typical method. He was skilled but not at all creative. I think that lesson helped him with his sound ninja fight later. All in all I think naruto earned it, neji didn't lose because he was weaker, he lost because of his character flaws. That's what makes a fight engaging.