The 21-year-old had long been touted as the young pretender to Kenya's steeplechase crown but he produced a final lap sprint that carried him to gold in an Olympic record of eight minutes 3.28 seconds.
A winner of two silver world championship medals, Kipruto was so far ahead of his rivals that he started celebrating and waving to the crowd at the start of the final straight.
"Even before the race I knew I would win," said Kipruto, who revealed he had suffered a calf injury days earlier.
The victory was the first time in a major competition that Kipruto had defeated Kenya's double Olympic champion Ezekiel Kemboi, who announced his retirement after finishing third - an honour the judges later stripped him of after finding he had stepped out of his lane.
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Before that decision, Kipruto thanked 34-year-old Kemboi for inspiring him over the years and promised to work hard to ensure Kenya's record of winning consecutive Olympic gold medals in the 3,000m steeplechase.
"I'm ready to take up the mantle," he said.
The African nation has now won every 3,000m steeplechase final it has competed in since 1968, having boycotted the 1976 and 1980 Olympics for political reasons.
Evan Jager won a rare medal for the United States in the race - their first since 1984 - after overtaking Kemboi in the last 50m to take silver.
"I just tried to stay as relaxed as I possibly could and hang on to Kemboi. He kinda looked back at me...on the back stretch, and I knew at that moment I might have him," Jager said.
"That was total joy."
Kemboi won his fourth steeplechase world championship title in a row last year.
"After 18 years I have done my best," said Kemboi, who won gold at the Athens and London Games. He could not be reached for immediate comment on the decision to disqualify him.
France's Mahiedine Mekhissi was elevated to third place.
(Additional reporting by Scott Malone, Editing by Mitch Phillips and Ed Osmond)
