Having sizzled with an opening five-under 67, co-overnight leader Sekito could only manage a second straight 74 to finish level with D’Souza in regulation play on one-under 215.
Both players traded birdies on the first play-off hole before D’Souza, one of Hong Kong’s up-and-rising amateurs, capitalised with a par on the next hole to put an end to the pulsating contest.
Thailand’s Amarin Kraivixien was placed third on 218, one stroke clear of compatriot Parathakorn Suyasri.
After a string of runner-up finishes this year, D’Souza was delighted to cap his season with a breakthrough international title
"I was striking the ball well all week and my solid start kept me in contention. I have been to Malaysia many times before for other tournaments but to win this particular championship on my first attempt on this golf course is something to cherish,” said the long-time Hong Kong junior international squad member, who opened his campaign with matching 72s.
He traded four birdies and three bogeys to make the turn on 35 but failed to convert his chances on the back nine as he returned with nine pars.
"I hit nine greens in regulation on the back but couldn’t find a birdie, which was a minor disappointment. But I bounced back strongly in the play-off, whatever nerves I had dissipated when I sunk the birdie on the first extra hole. It was 50-50 between Naoki [Sekito] and myself and I didn’t crack under the pressure,” said D’Souza, who received the Tan Sri Azman Hashim challenge trophy, named after the founder and chairman of title sponsor AmBank Group.