Haha! I used that same trick! Then I showed my friend who couldn't beat him and he was like, "Oh my gosh! I could've done that all along?" He got so mad...
Yeah, that really does the trick! Also in the 3DS version, I think that he goes back faster into his hole if you do that, especially if he has the fire-breathing phase.
And of course a jump slash with the Biggoron's sword is the way to go because it does 4x (or 3x?) the damage of a normal Master Sword slash and you only have one hit per turn so this pretty much maxes out the damage per turn.