The tug on his hand seems to do the trick. Inigo emerges from the water again, sucking in the deepest breath he's ever had, like his lungs were completely deprived of oxygen down there.

"T-- Tidus.."

Give him a moment, he's speaking between heavy breaths here, his eyes wild.

"I-- I did it! I held my breath down there! I have become a new person!" See here: the solution to the mystery of why Inigo didn't get back up after the five seconds. He forgot to count in his head because he was busy having a dumb dramatic revelation down there.