Japan crossed the line in 2 hours, 5 minutes, 58 seconds in the six- leg 42.195-kilometer race, which was contested by 15 teams from 13 countries and mixed three men with as many women.
A select team of Japanese university students followed in second in 2:07:47, while Kenya, featuring reigning world marathon gold medalist Abel Kirui and Beijing Olympics silver medalist Catherine Ndereba, took third in 2:08:34.
Japan's Yuichiro Ueno surrendered the lead to Australia's Craig Mottram in the opening leg but Yuriko Kobayashi rallied to win the next leg to give Japan the lead that Kensuke Takezawa, Yukiko Akaba, Atsushi Sato and Yurika Nakamura held until the end.
"This was the first time that I crossed the finishing tape," said anchor Nakamura. "I could run my part in a relaxed way because of the big lead that the previous runners gave me."
Takezawa, Akaba and Sato topped their respective legs while Mottram and Hikari Yoshimoto of the select university team timed the best in first and sixth.
Akaba matched a record in the fourth leg by completing the 5-km span in 15:34.
Beijing Olympics gold medalist Constantina Dita competed for the Romanian team, which came in 10th.