The veteran 35-year-old, a two-time doping offender, recovered from a poor start in Kawasaki to win the Golden Grand Prix in 10.28 seconds into a slight headwind as he pipped Japan's Aska Cambridge by three hundredths.
Japanese hope Abdul Hakim Sani Brown struggled home in fourth in 10.42 behind Shuhei Tada (10.35), while China's Su Bingtian failed to build on victory in Shanghai earlier this month as he slumped to fifth.
"I've been a little injured so I haven't been able to train as hard as I want to," Gatlin told reporters. "But I've been working on my top-end speed and my finish and that helped me out today."
