Three-times London champion Martin Lel of Kenya finished second for the second year in a row, just ahead of Ethiopian Tsegaye Kebede.
Kipsang clocked 2:03:42 in Frankfurt last year, four seconds outside compatriot Patrick Makau's world record. Makau dropped out of Sunday's race around the halfway mark.
The elite men went through the halfway stage shortly after Tower Bridge in 62 minutes 12 seconds, at which stage Kipsang surged to the front. He accelerated again at 35 kms to take an unassailable lead.
(For more sports news and updates, follow Ahram Online Sports on Twitter:@AO Sports)