Tokai University came from behind to win the Tokyo-Hakone ekiden for the first time on Thursday.
Tokai University, starting 1 minute, 14 seconds behind Wednesday's first-day leader Toyo University, clocked a total time of 10 hours, 52 minutes, 9 seconds for the two-day, 10-segment round trip from Tokyo to Hakone, Kanagawa Prefecture.
"I'm still having trouble believing, but I'm very happy. All 10 runners were confident in what they've been doing until now and demonstrated it," Tokai University coach Hayashi Morozumi said.
Aoyama Gakuin University was runner-up, missing its chance to become the third school in history to win the annual race five consecutive years.
The school started Thursday's 109.6-km return leg in sixth place but narrowed the gap to finish 3 minutes, 41 seconds behind Tokai.
Toyo University, the 2014 champion and overall runner-up the past three years, finished third in the 23-team race.
Tokai University, competing in the men's race for the 46th time, was fifth last year.
"We've had frustrating results in the past, but the fact that the runners never gave up bore fruit," Morozumi said.
Ryohei Sakaguchi, Tokai's second runner of the day, closed the gap with Toyo to four seconds in the seventh stage, and Yohei Komatsu rewrote the eighth-stage record to take the lead.
Twenty-two universities and one unified team from Kanto competed in the 95th edition of the race.