Kapur parred 14 straight holes before hitting back-to-back birdies on the 15th and 16th to seize the outright lead on nine-under 204 at the 150 million Yen (approximately USD 1.27 million) event sanctioned by the Asian Tour and Japan Golf Tour.
Overnight leader Kodai Ichihara of Japan, chasing a first career win, posted a 71 to trail by one-shot while a host of proven champions including Marcus Fraser of Australia and K.T. Kim of Korea are two shots back at the Chiba Country Club, Umesato course.
After making a stretch of pars including a huge 40-feet putt on the eighth hole, Kapur stayed cool under pressure to give himself a fighting chance to end an 11-year title drought on the Asian Tour.
"It is a great feeling to lead in a tournament. At the start of the day, the goal was to keep doing what I've been doing. It was a battle of patience for me because the putts didn't fall," said Kapur, who recently tied the knot on April 3.
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Kapur hopes to keep a level head in the final round as he aims to become the third Indian after Jeev Milkha Singh and Jyoti Randhawa to win in Japan.
"It is never easy to win a tournament. You have to go out and play good golf. You can't play average golf and win. Whether it is 10 or 15 guys in contention I have to go out there and play good golf," said Kapur.
Fraser, who won in Malaysia in February to top the Asian Tour Merit rankings, fought back from a poor start where he was two-over after eight holes to return with four birdies and one eagle for a 67.
The highly rated Thanyakon enjoyed a hot-putting streak, needing only nine putts in the first nine holes highlighted by five birdies. He marked his card with another birdie on 14 to charge into contention for a first Asian Tour title.