Defending champion Stanley Biwott of Kenya withdrew at the 10-mile mark with a right calf injury. He also dropped out in the Rio Olympics after getting sick.
American Abdi Abdirahman placed third.
Desisa, who was the runner-up in New York in 2014 and a two-time Boston Marathon winner, dropped out at the 22nd mile.
Tatyana McFadden won the women’s wheelchair race to sweep the four major marathons for the fourth straight year.
The 27-year-old American finished with an unofficial time of 1:47:43. She completed the Grand Slam by winning in London, Boston, Chicago and New York, extending her record streak to 17 straight wins in major marathons.