Naruto was not using a full-powered Rasengan vs. Sasuke's overpowered Chidori.
Obviously, Naruto's fox cloak is and was way stronger than Sasuke's cursed seal levels, and it has been said and proven that Rasengan is more powerful than Chidori.
The ONLY reasons Sasuke won was because:
1)Naruto was not trying to kill Sasuke, he loved Sasuke like a brother and viewed him as his brother, as said many times in the manga/anime. Would you be able to kill yourr brother or go all out on him if he were leaving your village?
2)Naruto was holding back his full power with his rasengan. We all know that rasengan is stronger than Chidori.