Kotut, 23, finished in an official time of 2hr 07min 10sec, well short of Kenenisa Bekele's course record from two years ago but comfortably clear of fellow Kenyans Laban Korir and Stephen Chemlany.
Kotut was one of eight runners in contention after 35 kilometres, before Ethiopia's Gebretsadik Abraha upped the pace heading into the final 4km.
Kotut then pulled clear shortly afterwards and held off his challengers as he cruised across the line.
Visiline Jepkesho, also of Kenya, claimed the women's title in 2hr 25min 52sec, ahead of Ethiopian pair Gulume Chala and Dinknesh Tefera.
Jepkesho ran a slower time than when she finished third in last year's race and was almost five minutes behind the course mark set by Boru Tadese of Ethiopia in 2013.