Chumba, wearing a bright yellow singlet, clocked 2 hours 9 minutes 25 seconds as twice runner-up Kitwara recorded his fourth consecutive top-four finish, placing 25 seconds behind.
Chumba broke up a tactical race with a surge after about 30km and gradually increased his lead over Kitwara.
"The race was good, but the pace was slow to 30km," said the 28-year-old, who won the Tokyo marathon in 2014 and finished third there this year.
Kenyan Sammy Ndungu took third in 2:10:06, followed by Ethiopian Girmay Birhanu Gebru and surprising American Luke Puskedra.
