The 27-year-old Miyazato fired an impressive 7-under-par 64 in the final round to lift the title by one stroke at Naha Golf Club with his four-day aggregate of 14-under-par 270. He won $191,980.
Overnight leader Singh stumbled to a 73 for tied second place with five other golfers, including Korea's Charlie Wi and Australian Scott Barr, who both closed with matching 68s.
'Am I dreaming?' said a jubilant Miyazato, who hails from Okinawa. 'Before the tournament, I just aimed to do best and not to finish lower than my brother Yusaku (who was also in the field).
'Winning my first Japan Golf Tour title in my home town is a great feeling. I want to thank my friends and the people of Okinawa who came out today to support me and it really made me relaxed out there,' added Miyazato, who had played in the Qualifying School in the last two years.
Starting the day eight off the pace, Miyazato's eight birdie round vaulted him to his maiden career title in the $830,000 Okinawa event which is jointly sanctioned by the Asian Tour and Japan Golf Tour.
It was truly a family affair for Miyazato as his brother Yusaku, who finished tied second here last year, played the weekend rounds, finishing tied 56th this time around and his younger sister Ai, a professional golfer as well, was one of the TV commentators.
Singh, who led by four strokes entering the last round, bogeyed his last hole to let slip a great chance of ending a five-year title drought. He turned in 1-under par but a double bogey on the par-5 10th left him with an uphill battle.
Singh bogeyed the 16th but got the shot back at the next hole with a birdie before his last-hole heartbreak. He was the only player in the top-20 to shoot over par in the final round.
First round leader Wi, who recently secured his PGA TOUR card, had six birdies against three bogeys as he finished tied second for the second consecutive year in Okinawa. Japan's Mamoru Osanai, Hideki Kase and Masahiro Kuramoto also finished joint second on 271.
The Okinawa Open is the first counting event for 2005 for the Asian Tour and Japan Golf Tour.