The 26-year-old Biwott clocked two hours five minutes 11 seconds over 42.195 km to beat fellow Kenyan Vincent Kipruto's previous Paris mark by 36 seconds.
"The pace was a bit slow and I knew if I could up the pace a little but I could win it. And when I went, I knew I was going to win it," Biwott told French TV channel France 3.
Ethiopia's Girima Assefa was second, crossing the finish line on Avenue Foch one minute 12 seconds behind on a chilly morning.
Ethiopian Tirfi Beyene won the women's race in a Paris record of two hours 21 minutes 39 seconds.