He broke the previous world record set in Berlin by Kenyan Dennis Kimetto in 2014 by 1 minute and 18 seconds an improvement that had not been witnessed in fifty years.
Kipchoge's run was the biggest improvement on the marathon mark since Australian Derek Clayton took nearly two and a half minutes off the record in 1967.
After the race, Kipchoge, who also won in 2016 and 2017, said: "I lack words to describe this day. I am just so incredibly happy to have finally run the world record as I never stopped having belief in myself".
"They say you can miss it twice but not third time".
If it was expected that Kipchoge would be slowing down as the race progressed, then "the great philosopher" went exactly the opposite direction. "I will come back next year", he said.
"I had great belief that I could achieve this feat and running a sub 2 hours two minutes was simply incredible and I believe I can still go below that with such good conditions".
Kipchoge, who previous year took part in the Nike Breaking Two project, where he ran two hours and 25 seconds with the aid of "illegal" in and out pacemakers, started off at a sizzling pace.
He started off with a sizzling pace and quickly shook off his biggest opponent, Wilson Kipsang, to make it a one-man race.
His three pacemakers were pushed to the limit to keep the tempo high as Kipchoge dipped well below world-record time at the halfway mark.
Most observers feared that had left Kipchoge's hopes of a world record in the balance.
"I've run 2:00. I have run 2:01. That's what pushed me in the last kilometres", added Kipchoge".
But the race conditions at the Nike-sponsored event were so favorable - Kipchoge ran behind a six-man pace-setting team and was trailed by a time-keeping vehicle on a racing circuit in Monza, Italy - that the time was not recognized by the International Association of Athletics Federations (IAAF).
Amos Kipruto of Kenya was second in 2:06:23 with Kenya's Wilson Kipsang, the former world record holder, third in 2:06:48.
And on a pleasant autumn day in Berlin the 33-year-old lived up to that billing - and more - as he proved beyond doubt that he is the greatest long distance runner in history by obliterating the marathon world record. Kipruto and Kipsang's times are an indication of how Kipchoge's pace blew the race apart from the outset.