Yes, he had to use the chibaku tensei to seal him, which was costing him, but he was not against doing it, despite konan's protests. Naruto was beginning to transform into full 9 tails, that is what was breaking him out, not 6 tails or even 7, it was 8 tails that broke free, then minato restored his chakra and health, and even then pein was still giving him a very hard time.
That's what you have to consider here: First, a full power and full health naruto arrives on the battlefield, takes out the other peins, but the davapath locks him down via rinnigan rods. Then he goes kurama berserk, gives Pein a bit of a headache and problem, but Pein pulls out his chibaku tensei to hold him, losing more power and health declining. Then Naruto is again, at full power and health due to minato, and pein was still able to hold his own and force naruto to use his unique prank style fighting to defeat him.
That is essentially 3 tries naruto had against pein, who was already weakened. So that's my point... if Pein was not weakened, it is likely naruto would not have won without the help of tsunade and company. Now I am not downplaying naruto in the least here, because in sage mode he had Pein on the ropes, but since he was not used to it, he couldn't use sage mode to its fullest extent yet.
