The 24-year-old clocked a winning time of two hours, six minutes, 58 seconds with Japan's Hiroyuki Horibata runner-up in 2:08:24 and Henryk Szost of Poland third in 2:08:42.
"I never imagined I could win this race," the Japan-based Gitau told reporters after his first marathon victory. "My past results haven't been good.
"But I wanted to sharpen my focus on the marathon and I've been running in Japan since high school so the environment suits me."
Gebrselassie ran in February's Tokyo Marathon in a bid to launch his bid for an Olympic swansong in London but flopped to a fourth-place finish and eventually failed to make the cut.
The 39-year-old Ethiopian, twice Olympic and four-times world 10,000 metres gold medallist, had even less joy on his return to Japan.
Among the leading group of six runners, Gebrselassie pulled up at the side of the road with around 10 kilometres left.
Gebrselassie's latest failure is set to further fuel speculation over the future of the man dubbed the "Emperor" after another year of disappointment.
Kenyan athletes won both the men’s and women’s elite categories in the Standard Chartered Marathon in Singapore .
Men’s victor Kiproo Lilan Kennedy was the first across the tape with a time of 2 hours 17 minutes 20.27 seconds, ahead of compatriot Luke Kibet, who crossed five seconds later at 2:17:25.25.
Kibet holds the course record of 2:11:25 – a good six minutes clear of Kennedy’s finishing time.
Barmao Samson Kiprono made it a clean sweep for Kenya, clocking 2:17:30.52.
Fellow Kenyan Irene Jerotich Kosgei notched her third Singapore title in the women’s event with 2:37:53.51, ahead of Kenyan Flomena Cheyech and Alina Prokopeva of Russia who finished in 02:37:56.51 and 02:38:33.70 respectively.
The world’s oldest marathoner, 101-year-old British man Fauja Singh, participated in the 10km event.