Hiroyuki Akimoto defeated 2013 world champion Shohei Ono on points to claim the title in the men's 73-kg category at the Grand Slam Tokyo on Saturday.
The 28-year-old Akimoto captured the title for the first time in three years and second time overall.
"I fought with guts, persistence," said Akimoto, who won the world title four years ago.
In the absence of reigning world champion Riki Nakaya, Akimoto scored ippon victories in all five matches before facing Ono but was first to fall behind with a shido with nearly one minute left in the final. He executed a seoinage throw for yuko as time ran out.
"I pressed ahead with my spirit. I am a gritty judoka," he said.
At 81 kg, 21-year-old Takanori Nagase scored an ippon against world champion Avtandili Tchrikishvili of Georgia in the semifinals en route to defending his title by beating Sergiu Toma of the United Arab Emirates in extra time in the final.
On the women's side, London Olympian Haruka Tachimoto had to settle for the silver medal after falling to world champion Gevrise Emane of France in the 70-kg final.
World silver medalist Karen Nun Ira came up empty-handed after a defeat in the quarterfinals. She won her first repechage match, but fell to Canada's Kelita Zupancic in the match for third place.
At 63 kg, Maho Nishikawa earned a bronze medal, but world bronze medalist Miku Tashiro and 17-year-old Miho Minei crashed out in the second and first rounds, respectively.
After two days of competition, the host has won three weight categories in both the men's and women's brackets.