The 39-year-old Kipchoge faded badly at around the 20-kilometre mark and crossed the line in 2’6:50s.

Kenya’s Kipruto won in a course-record 2’02:16s ahead of countrymen Timothy Kiplagat (2’02:55s) and Vincent Ngetich (2’04:18s).

Ethiopia’s Sutume Asefa Kebede won the women’s race in 2’15:55s, ahead of Kenya’s defending champion Rosemary Wanjiru (2’16:14s) and Ethiopia’s world champion Amane Beriso Shankule (2’16:58s).

Sifan Hassan of the Netherlands was fourth after clocking 2’18:05s.

The race took place less than a month after world record-holder Kelvin Kiptum died when his car crashed into a tree in Kenya.

Kiptum was killed at the age of 24 on Feb 11, just months after he beat Kipchoge’s world record to set a new mark of 2’00:35s in Chicago.

Kiptum and Kipchoge were expected to face off for the first time at the Paris Olympics.

The Tokyo Marathon was Kipchoge’s first race since Kiptum’s death and he was on pace to reclaim the world record at around the 15km mark.

But he dropped back dramatically to leave Kiplagat, Kipruto and Ngetich fighting it out in the leading pack.

Kipchoge continued to struggle as the race wore on and had dropped out of the top 10 by the 35km mark.

Kipruto took over the lead from Kiplagat around 30km in and powered towards the finish for a new personal best.

Kiptum was driving in the Rift Valley, the heartland of Kenyan distance running, when his car careered off the road.

Police said Kiptum and his Rwandan coach Gervais Hakizimana were killed on the spot while a woman passenger was injured.