Kipyegon shattered the world record in the 1500m in Florence last week and kept her nerve over the longer distance to win in 14min 05.20sec, slicing a full second and a half off the previous best of 14:06.62 set by Ethiopia's Letesenbet Gidey, the world 10,000m champion.
"No, I did not think about the world record, I do not know how I made it," said Kipyegon, who burst into tears after crossing the line.
"I just focused on the green light and tried to stay relaxed and enjoy the race.
"I just did the race and wanted to see what happens. When I saw that it was a world record I was so surprised. It was all about giving my best. I just wanted to improve on my personal best, the WR was not my plan."
The field was aided by three pacesetters, including Kenyan Beatrice Chepkoech, another world record holder, albeit in the 3,000m steeplechase.
Carefully following the trackside lighting system that indicated world record pace, Kipyegon hit the front with 700m of the 12-and-a-half lap race to run.
Gidey stayed on her heels as the Kenyan, a double world and Olympic champion over the 1500m, went through the bell in front.
The Ethiopian threatened to hit back coming into the final 200 metres, but Kipyegon accelerated away down the home straight in an absolute masterclass of distance running, just as she did in Florence last week.
Gidey finished second in 14:07.94 with another Ethiopian, Ejgayehu Taye, the world record holder over 5km, coming in third (14:13.31)
Kipyegon had been scheduled to return for a training camp in Kenya before returning to Europe for another potential record attempt over 1500m at the Monaco Diamond League meet on July 21.
But after her second world record, she said: "I do not know what will be next, I still have to discuss it with my coach and my management.
"I am so happy, I am very emotional right now and do not know what to say. If my body is healthy, anything is possible."