Britain's Mohammed Farah won the day's other gold medal with a victory in the men's 10,000 meters that ended Ethiopia's winning streak in the event in the past five Worlds.
Kiplagat overcame a slow start and overtook gutty Italian Valeria Straneo at the 40 kilometer (24.8 mile) mark before sprinting down the stretch to a 2 hour, 25 minute, 44 second victory, 13 seconds ahead of Straneo.
Kayoko Fukushi placed third with a 2:27.45.
Straneo was the early leader in the 26.6-mile epic and set a fast pace as Kiplagat labored as far back as 15th place. Straneo said she eventually began feeling pain in her leg and could not prevent Kiplagat, who seemingly got her second wind, from cruising past her and going on to the gold medal.
"I got confident I was going to win at 40 km, when I started to increase my pace," said Kiplagat, who added the late starting time had required her to adjust her pre-race training.
Farah said his training regime was long and hard, but paid off with a gold medal after he had won the silver at the last Worlds in South Korea. "I've put a lot of work into it," he said. "I have been away from my family a lot, so that even my twin daughters don't recognize me, they think I'm a stranger."
Farah made himself a familiar face to track fans with a time of 27 minutes, 21.71 seconds. He edged defending world champion Ibrahim Jeilan of Ethiopia, who came in at 27:22.23.
Farah took advantage of the relatively slow pace of the race to turn on the gas at the bell and complete the final lap in 54.5. Paul Tanui of Kenya placed third.
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