Muniyappa overcome three bogeys, two of them on the back-nine, before the birdie on the final hole allowed him to break away from a five-way tie at the top of the leaderboard. Muniyappa's one-under 71 gave him a three-round total of 10-under 206.
Four players are one stroke back. Indians Harinder Gupta and Digvijay Singh, Marcus Both of Australia and South Korean Lee Sung all share second on a nine-under 209.
Gupta and Both shot identical five-under 67s in the third round to climb into contention, while Lee slipped from his joint-first place on Friday.
Muniyappa, who has not won an Asian Tour event, was at one stage summoned by the referee, who had to make a decision on whether Muniyappa's ball had moved when the player removed a chocolate wrapper lying next to the ball.
"I was a little nervous when the referee called me into the cabin," said Muniyappa, who avoided a two-stroke penalty when the referee ruled that the ball had not moved.
"I didn't putt well today, but I'm quite desperate to win this title and also to save my Asian Tour card," said Muniyappa, who is currently placed No. 97 on the tour.
Muniyappa is hoping to avoid a return to playing in qualifying rounds with a tour victory.