Donaire claimed his 29th successive victory when knocking Nishioka down in the sixth round and again in the ninth.
A swift uppercut to Nishioka then forced referee Raul Caiz to stop the fight as the Japanese fighter saw his own run of 16 straight wins come to an end.
"When you do engage, you open up yourself," Donaire said. "Nonito is a surgeon. I can pick them apart, and then the demolition comes later.
"I was just playing possum to see what he'll do. I wanted to open him up and time the jab, and that's exactly what happened."
Donaire's victory was preceded by a sensational fight between Brandon Rios and Mike Alvarado as the former stopped the latter in the seventh round.