After losing the first set to qualifier Zverev, the older brother of Alexander Zverev who stunned Novak Djokovic in the Rome Masters final, three-time Grand Slam victor Wawrinka needed 2 hours 20 minutes to seal victory.
Still, Zverev beat the third-ranked Wawrinka when they last played, at the Swiss Indoors in Basel in October.
"There haven't been too many times that I'm down match point and win, so it's great for me", said the Japanese.
Zverev, who came through qualifying, still seeks a first career title at age 29.
The Frenchman, who had been struggling with a shoulder injury, won the final 7-6 (7/2) 7-5 against Tomas Berdych, saving two set points at 4-5 in the opening set.
Meanwhile, Jo-Wilfried Tsonga prepared for the French Open in flawless style by claiming his maiden clay court title, beating Czech Tomas Berdych 7-6 (2) 7-5 in the Lyon Open final on Saturday.
Meanwhile, Kiki Bertens of the Netherlands won Nuremberg's WTA clay-court tournament for the second year in a row after her 6-2, 6-1 victory over Barbora Krejcikova in yesterday's final. "I had a great week after a hard period on a physical level, picking up a shoulder injury while I was in fine form".
The 13th-ranked French player will move up to 11th in the world in Monday's ATP rankings.
Stanislas Wawrinka and Jo-Wilfried Tsonga warmed up for the French Open with gutsy victories in their respective ATP finals on Saturday.