How did Naruto learn the Teleportation Jutsu? I distinctly remember that scene from the anime where Naruto has just learned to control the Nine Tail's chakra. He immediately senses Kisame hiding in the sword and goes on to teleport to him and give him a good punch.

Has it ever been explained how he suddenly knows how to use this jutsu? Is it maybe just the body flicker technique that was taken to new heights because he now has all this extra chakra or is it the teleportation jutsu in the same vain his father used?
I think you are talking about Chapter 505:


  Naruto Uzumaki completes his training of gaining the Nine-Tails'
  chakra inside of him. Before Yamato, Naruto, and Killer B leave,
  Naruto senses Kisame Hoshigaki inside Samehada. Samehada springs into
  action but Naruto used his right hand to smash Kisame.


There is no way that Naruto has used teleportation technique. But when someone does jinchūriki transformation, then according to wiki:


  The user's physical abilities are enhanced while the mode is active,
  with greater enhancements coming from using more of the Nine-Tails'
  chakra.


So by simply doing a jinchūriki transformation, I don't think he will be able to teleport all of a sudden, and there is also nothing in wiki which states that he was able to do teleportation. So it was his greater speed!