Both players finished the weather-shortened US$6 million championship, sanctioned by the Asian Tour and European Tour, tied on 14-under-par 199 after the third and final round at the Sentosa Golf Club's Serapong course.
They hit their second shots onto the fairways at the sudden-death play-off when torrential rains and lighting struck again, leaving the two to resume their battle on Monday.
When play finally resumed, it was the Spaniard who finally got the better of the Filipino who could have delivered the knockout blow had he not missed a short birdie putt at the first play-off hole.
"It was very close. I thought I was going to make my first putt (on the first play-off hole)," said Pagunsan, whose lone Asian Tour victory was in 2007.
After hitting their third shots to within 10 feet of the pin at the second play-off hole, Pagunsan missed his birdie putt while Fernandez-Castano reeled in his to end his three-year title drought.
"I read the putt really good and hit my putt really good but the ball did not break much when it was close to the hole it went straight when it was supposed to turn left," said Pagunsan.
For Fernandez-Castano, it was a welcome relief, having squandered a four-shot lead heading into the final round and being able to prevail at the end.
"It has been a great relief, especially the way I played yesterday, having a four-shot lead and spoiling it all. It has been a tough year and I got a monkey off my back. It has been three years without a victory and it means a lot to me," said Fernandez-Castano.