Dead hand appears first in the Bottom of the Well ... he's the enemy you defeat to get the lens of truth. He also makes an appearance in the Shadow Temple .. the mini boss you fight to get the Hover Boots. So you did fight him, as you can't beat the game without the Hover Boots and it's VERY tough to beat without the lens of truth.
It was this guy:
His hands coming up from the ground grab you by the head when you get close to them, and you have to wiggle free as he comes up from underground and approaches you. When he's close, he lowers his head slowly (which is when you hit him), and after hitting him he burrows back underground until you get grabbed by one of his hands again.