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Norway's Alexander Dale Oen, who had been fastest in the qualifying rounds, finished second in 59.20, with France's Hugues Duboscq third in 59.37.
Hansen, who was second at the turn, had to settle for fourth in 59.57.
The event was expected to be a showdown between Kitajima and Hansen, who had not been defeated since losing to Kitajima in Athens and had the fastest time of the year in the world coming into Beijing.
But it was Oen who was the swimmer to beat after setting consecutive Olympic records in the preliminary round and semifinals.
Oen had a slight .12 second lead coming off the turn, but Kitajima poured in on down the stretch to touch first and add another chapter to the story of his sparkling career.
The 100m breaststroke is considered the weaker of Kitajima's two events and prospects are high that he can complete the double when the final of the 200m race is held Thursday.
Meanwhile, a short time earlier, Zimbabwe's Kirsty Coventry set a world record in the semifinals of the women's 100 backstroke, clocking 58.77 seconds to cut .20 off the previous mark set by American Natalie Coughlin in July.
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