By finishing in the top two, and running quicker than the qualifying standard, 27-year-old did what was required for a spot at her third Games, having finished 21st overall in the heats at London 2012 before winning gold in Rio.
Kipyegon's performance sets up a potential tussle against world champion Sifan Hassan of the Netherlands in Tokyo.
"My focus is to defend my Olympic title in Tokyo," Kipyegon said afterwards in quotes reported by Athletics Kenya.
"It was a really good race here, which I really wanted to win. I know I will meet many good athletes in Tokyo but I have prepared really well."
Earlier, Lilian Kasait and Rio 2016 silver medallist Hellen Obiri secured Kenya's two direct Tokyo 2020 berths in the women's 5000m.
The top seven finishers all went under the qualifying standard time of 15:10.00, but with Athletics Kenya only awarding qualification to the top two, it was Kasait (14:52.18) and Obiri (14:52.51) who crossed the line in the required positions.
"I didn’t expect to win," Kasait said. "The [race] was tactical. I didn’t have many races but my preparations [were] uninterrupted. My wish is to ensure we work as a team in Tokyo to ensure we deliver podium finishes."