Two judges scored the bout 118-109 for John, recently named the WBA's fighter of the decade, with the third awarding it 117-110 to the undefeated Indonesian, much to the delight of the 4,000 fans at Marina Bay Sands Integrated Resort in Singapore.
Barring a slight wobble in the seventh when Kimura rocked John with a big left hand, the Japanese offered little in attack as the 32-year-old Indonesian improved his record to 47-0-2 (22 knockouts).
"Yes, it was a big shock," John told Reuters of Kimura's sole telling blow which cut the champion. "I needed time, I did well to recover."
Asked if he was happy with his performance John replied: "Could do better."
John, making his first defence in Singapore, was a heavy favourite against his overmatched opponent Kimura (24-4-2, nine knockouts), who was content to just survive the 12 rounds against his more skilled adversary.
After landing a couple of sharp jabs and big uppercuts in the second round, John walked to his corner - arms aloft - sure his defensive-minded opponent had little chance of claiming his title.
John continued to press through the rounds but many of his blows landed only on the gloves of the 34-year-old Japanese.
The fight then came to life in the seventh when Kimura landed a heavy left hook which wobbled John, whose legs looked shaky, drawing gasps from the many Indonesians in the crowd.
However, John recovered as Kimura failed to follow up and returned to his defensive ways with the Japanese being booed heavily by fans in the later rounds for holding.
The victory against his outclassed opponent will do little to appease the Indonesian's critics, who feel the talented John should fight more in the United States, the traditional home of the sport, against better-ranked fighters.
Earlier, Indonesia's Daud Jordan claimed the vacant IBO featherweight title when he recovered from a knockdown in the opening 20 seconds to stop Filipino Lorenzo Villanueva in the second round.
Jordan's record improved to 29-2 (23 knockouts) while Lorenzo suffered the first defeat of his career and slipped to 22-1 (21 knockouts).