Kobayashi matched the second best nine hole score of seven-under-par 28 on the Asian Tour for nine-under-par 62 and a winning total of 17-under-par 267 at the Higashi Hirono Golf Club.
Koumei Oda closed with 67 for second while Shiv Kapur of India and Juvic Pagunsan of the Philippines shared fourth place after shooting a 67 and 71 respectively at the 150 million Yen (approximately US$1.9million) event sanctioned by the Asian Tour and Japan Golf Tour.
Kobayashi, who earned his Asian Tour card at Qualifying School in Thailand earlier this year, battled to his first Asian Tour win with five birdies and one eagle on the front nine followed by three birdies and one bogey on the back.
"My dream was always to win on the Asian Tour and in Japan and I've enjoyed the best of both Tours. This is indeed a very happy occasion in my career," said the lanky 36-year-old, who won US$381,000.
Kobayashi, who was four groups in front of the leading flight, overcame a six-shot deficit but had to endure a nervy wait when he missed a tricky eight foot birdie putt on the last.
"When I missed that putt, I thought I was going to be in a play-off with Koumei (Oda). I was very nervous until fans started coming over and congratulating me because Oda made par on 18," he smiled.
"This win does so much for me because I get to play in all the events on the Asian Tour. There are many big events coming up so this win puts me in good position," added Kobayashi.
Reigning Asian Tour number one Pagunsan struggled early in the round as he was six-over after seven holes but produced a brave fight back to finish the day on even-par and four shots from the champion.
"I had a bad start. I missed a lot drives but I'm pleased with how I fought. It is a really nice comeback. I told myself I need to play good again and the birdie on eight was the turning point for me," said Pagunsan, who has won one Asian Tour title.
"It was disappointing but I can take pride with how I played. I learned a lot about myself and next time I need to stay patient and calm when I'm in this position again," added the Filipino, who was one shot off the lead at the start of the final day.
Kapur played with Kobayashi and rode on the momentum as he claimed his third top-five finish on the Asian Tour with a round of five birdies and one blemish.
"We were trying to match each other shot-for-shot. He kind of got hot in the middle and ran away from me. My personal goal was to get to 15 or 16-under. I thought if I do that, then I might have a chance and I came up just short," said Kapur, a winner on the Asian Tour.
"I've been up there on the leaderboard lately and had something to prove to myself. I wanted to carry the form for four rounds. Being on the leaderboard and not finishing the job has been disappointing but this week was nice," he added.