Frenchman Jimmy Gressier finished in second 27 seconds behind first place.
Controversially, Cheptegei was wearing the Nike Vaporfly shoes - the pair of runners that Eliud Kipchoge wore during his sub two-hour marathon run.
Reports in January suggested that governing bodies were considering banning the shoe due to potentially performance-enhancing qualities. However World Athletics President Sebastian Coe confirmed athletes were still permitted to wear the shoe.
“As we enter the Olympic year, we don’t believe we can rule out shoes that have been generally available for a considerable period of time,” World Athletics president Sebastian Coe said.
“But we can draw a line by prohibiting the use of shoes that go further than what is currently on the market while we investigate further.”