The French Open champion exacted revenge on Japanese wildcard Tatsuma Ito, who had sent the muscular top seed tumbling out of the Tokyo tournament at the first hurdle 12 months ago, with a tough 6-3, 2-6, 6-4 second-round victory.
No such effort was needed from title-holder Kei Nishikori, who toppled giant American Sam Querrey 7-6, 6-3 to reach the quarterfinals despite failing to really catch fire.
Wawrinka pressed self-destruct after rolling through the first set, Ito levelling with a lunging forehand down the line that left the world number
four looking to the heavens in anguish.
Normal service was resumed in the decider, however.
A viciously dipping return onto Ito's shoelaces secured Wawrinka an early break and allowed him to play with a little less tension.
Wawrinka finally ended Ito's brave resistance on his fourth match point after an hour and 42 minutes with a fizzing forehand down the line.
"It wasn't my best match for sure," Wawrinka told AFP.
"I'm just happy to win. I struggled a little bit to find my rhythm but the most important thing for me was to get to the quarterfinals."
Second seed Nishikoro, dazzling in canary-yellow shirt, headband and sneakers, struggled with a swirling wind in the early skirmishes before
discovering his mojo in the first-set tiebreak, which he raced through 7-3.
Nishikori broke early in the second set and finished in style, belting a backhand down the line to set up match point and plunging home the dagger with an acrobatic smash.
He celebrated with a pump of the fist and a toothy grin at coach Michael Chang.
"It's always a mental battle against a big server," said Nishikori, who is bidding to win a third Japan Open in four years.
He next faces Croatia's Marin Cilic, the player who beat him in the 2014 US Open final.
"The first-set tiebreak was key," added Nishikori, who is chasing a fourth title of the year and the 11th of his career.
"After that I was able to relax a little and I think I played some pretty decent tennis."
Third seed Gilles Simon blew past Czech Jiri Vesely 6-4, 6-2 to reach the last eight.
"It's a very tough tournament to win," the Frenchman said of an event won in the past by such luminaries as John McEnroe, Ivan Lendl, Pete Sampras, Stefan Edberg and Roger Federer.
"It's not one you win by chance. It would be a great achievement but you need to be playing at a really high level."
Seventh seed Feliciano Lopez from Spain had nothing left in the tank after reaching last week's final in Kuala Lumpur and was dumped out 6-4, 4-6, 6-1 by Portugal's Joao Sousa in a first-round match.
Sixth seed Cilic won his opener against American Donald Young 7-5, 5-7, 6-4, while Luxembourg's Gilles Muller beat Frenchman Jeremy Chardy 7-6, 7-6 to set up a quarterfinal against Simon.