The Olympic champion and world record holder from Kenya clocked 1 hour, 59 minutes and 40.2 seconds at the INEOS 1:59 Challenge on Saturday, an event set up for the attempt.
Kipchoge, who compared his attempt earlier to a man landing on the moon, twice punched his chest in celebration and smiled when he finished.
"That was the best moment of my life," he said before adding that he trained four-and-a-half months for his extraordinary race against the clock. "The pressure was very big on my shoulders. I got a phone call from the President of Kenya. I am the happiest man today."
Kipchoge pointed out his mission went beyond athletics.
"We can make this world a beautiful world and a peaceful world," he said. "The positivity of sport. I want to make it a clean sport and an interesting sport."
Kipchoge was cheered by spectators along the course in Prater Park and there were celebrations in his home country before he had even finished.
"Hearty congratulations, Eliud Kipchoge," President Uhuru Kenyatta said in a statement. "You've done it, you've made history and made Kenya proud. Your win today will inspire future generations to dream big and aspire to greatness. We celebrate you and wish you God's blessings."
Hundreds of joyous Kenyans brought traffic to a standstill in the middle of the capital, Nairobi, as they gathered to watch the end of the run on a large screen. People pumped their fists, clapped and fell to their knees as Kipchoge cruised to the finish line.
In Kenya's running mecca of Eldoret, called the home of champions, hundreds of people burst on to the streets in celebration.
"We should line up the entire road from the airport to Nairobi. Receive him like the hero he is," prominent activist Boniface Mwangi said on Twitter.
Starting at 8:15 a.m., Kipchoge was supported by 36 pacemakers who accompanied him in alternating groups, one of the reasons the IAAF will not ratify the time as a world record.
The groups were also helped by a pace car with a laser beam, projecting the ideal position on the road, and they received drinks handed over by cyclists and other runners to prevent them from having to slow down.
Running at an average pace of 2:50 minutes per kilometer (4:33.5 minutes per mile), Kipchoge was 11 seconds ahead of schedule halfway through his run. He then maintained his tempo until the pacemakers left him for the final 500 meters, where he sped up.
"I was really calm, I was just trying to maintain the pace," said Kipchoge, adding he was never in doubt about breaking the barrier. "For me it was not 50-50, it was 90 percent."
Jim Ratcliffe, founder of the chemicals company backing the attempt, exchanged high-fives with Kipchoge after the finish.
"He even accelerated in the final kilometer, he is a super human," Ratcliffe said. "I can't believe he's done it. He did the first half in less than an hour and then he's just done that again."
Organizers said normal anti-doping regulations were in place and that Kipchoge and all the pacemakers were being tested in and out of competition by the Athletics Integrity Unit (AIU).
The team behind the event "has ensured all athletes involved in the project are undergoing extensive intelligence-led testing that has been pioneered by the partnership between Abbott World Marathon Majors and the AIU," they said in a statement to The Associated Press.
The Prater Park in the Austrian capital offered long straights, protected from the wind by high trees, for most of the 9.6-kilometer course, which Kipchoge completed more than 4 times.
It was his second attempt at breaking the two-hour barrier, after missing out by 26 seconds at a similar event on the Formula One track in Monza, Italy, in May 2017.
Kipchoge, who took Olympic gold in Rio de Janeiro in 2016 and has won 10 of his 11 marathons, holds the official world record of 2:01:39 since shattering the previous best mark by 78 seconds in Berlin last year.
I don’t know where the limits are, but I would like to go there. pic.twitter.com/ET2aZIoa2J— Eliud Kipchoge (@EliudKipchoge) October 11, 2019
In near-perfect circumstances at the meticulously planned attempt, Kipchoge shaved almost two minutes off that time.
Long-time coach and mentor, Patrick Sang, a former Olympic and world steeplechase silver medalist, said it was "really exciting."
"I am happy for him and what he has achieved. He has inspired all of us that we can stretch our limits and that we can do more than we think we can do," Sang added.
Under Sang's guidance, Kipchoge won gold in the 5,000 meters at the world championship in 2003, the start of a distinguished track career which includes Olympic bronze and silver medals from 2004 and 2008.
After missing out on qualification for the 2012 London Olympics on the track, Kipchoge switched to the marathon and has since been pushing the boundaries of the discipline.
Associated Press writer Tom Odula in Nairobi, Kenya contributed.