At the halfway point the back-to-back Olympic champion in Rio and Tokyo looked set to become the first to officially run under the elusive two-hour mark.
But despite slowing slightly the 37-year-old held on to best his own record from Berlin in 2018.
Kenyan Mark Korir finished second behind his countryman with a time of 2:05:58, while Ethiopian Tadu Abate came third with 2:06:28.
Ethiopian Andamlak Belihu, who kept up with Kipchoge for around two thirds of the race, held on for fourth.
Kipchoge, who on Friday said his only goal was “to run a good race”, burst out of the blocks, clearly aiming not only for a world record but to beat the two-hour mark.
A pod of around seven runners kept up with Kipchoge for the first 10 kilometres, before 2021 winner Guye Adola and Belihiu pulled away after 15 kilometres.
Adola was unable to maintain the pace and began to fall back after 18 kilometres, with both Kipchoge and Belihu reaching the half marathon mark in less than an hour.
Kipchoge emerged on his own after 25 kilometres and was still on pace for the sub-two-hour mark, but began to slow slightly despite still keeping the world record in his sights.
Kipchoge became just the second man to win four Berlin Marathons, joining Ethiopian Haile Gebrselassie who owned the event from 2006 to 2009.
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