He lost yet they both where on the ground unable to move.
Naruto didn't want to kill sasuke even at the start of the fight.Sasuke also noticed that naruto was slacking and holding back.All naruto was doing is to counter sasuke's attacks rather than trying to kill sasuke.In simple terms,Naruto was playing defensively rather than offensively.
When Sasuke lost his consciousness,Naruto didn't kill or attack him.Why do you think that naruto was waiting for sasuke to wake up?
Its not like naruto would die if he moved an inch.you should get this misunderstanding out of your mind.Naruto was saying that if they move "too much" they would die.Too much is the keyword here.
If naruto wanted, he would kill sasuke with the kunai when sasuke was unconscious but naruto didn't want to do it in the first place.
Naruto lost his motive to move that's why naruto stood still.