Cherono finished in two hours five minutes 45 seconds but British defending champion Farah placed eighth in 2:09.58 and previous winner Galen Rupp failed to finish.
The time was Farah’s slowest in a marathon by more than a minute.
He was not available for comment.
Both Farah and Rupp were formerly coached by the now-banned Salazar as was American Jordan Hasay, one of the women’s favorites who also did not finish.
Rupp suffered a calf strain about the sixth mile and he was forced to drop out near the 23rd mile, his management company said in a statement.
“Hasay felt a sharp pain in her hamstring after two miles, stretched and tried to continue, but was unable to,” the statement added.
The race was the first for the three since Salazar was banned from the sport for four years by the U.S. Anti-Doping Agency (USADA) for “orchestrating and facilitating prohibited doping conduct”.
Salazar has said he plans to appeal against the ruling.
Debela was a second behind Cherono and fellow Ethiopian Asefa Mengstu placed third in 2:05:48.
“Toward the end I felt like I could kick forward. I still had enough energy to sprint and it’s amazing,” Cherono said.
“I am so happy. It’s my second major marathon and to come only a few months after Boston is brilliant.”
American Daniel Romanchuk overwhelmed the men’s wheelchair field to defend his title in an unofficial 1:30:26.
The 21-year-old finished more than three minutes ahead of British runner-up David Weir.
Swiss Manuela Schar also retained her title, the 34-year-old winning the women’s wheelchair race in an unofficial 1:41:08.
Former champion Tatyana McFadden took second in 1:45:22.(Reuters/NAN)
(Edited by Olawale Alabi)