Waseda completed the 217.9-kilometer round-trip between Tokyo's Otemachi business district and the spa resort of Hakone in Kanagawa Prefecture in a new record time of 10 hours, 59 minutes, 51 seconds, wrecking Toyo University's hopes of a third consecutive title.
"It took a long road to get here. It's a double pleasure to win as a coach compared to winning as an athlete," said Waseda coach Yasuyuki Watanabe. "I didn't know what would happen until the final 400 meters but the amount of training we put into this, which was more than anyone else, paid off," he said.
Toyo, which led after Sunday's inward leg, followed in second place while Komazawa was third.
"Toyo was also amazing. It just goes to show you the difficulty of winning in the Hakone ekiden," Watanabe said.
Waseda's win, its 13th overall, made it only the third school to secure the triple crown of collegiate road relays after winning the collegiate invitational and the national championship last fall.
Daito Bunka won the first ekiden triple crown over the 1990-1991 season and Juntendo also achieved the feat in the 2000-2001 campaign.
Waseda trailed Toyo by 27 seconds after Sunday's five legs, but Hiroki Takano put his college in front in the middle of the first section of the trip back to the Japanese capital.
Waseda stayed in front until the finish, where anchor Kenji Nakashima's teammates were waiting to mob him as he approached the ribbon pumping his fists.
Toyo clocked 11:00:12 and Komazawa followed with a time of 11:03:53. Tokai, Meiji and Chuo took the next three spots.