Natipong Srithong carded a final-round 67 to close out the tournament on 15-under-par, which earned the Thai a one-shot victory.
Kruger, who won the 2012 Avantha Masters, shot rounds of 69, 65, 69, 71 at Manila Southwoods Golf & Country Club to finish sole second.
The final round was tough for the Bloemfontein local, who had his charge halted by a double bogey six at the 10th hole. It put him on the back foot over the stretch and, although he made a birdie at the 18th, he came up short of forcing a playoff.
“If it’s not meant to be, it’s not meant to be. I just hit a terrible shot on 10 and tried to fight back and hit it close a few times but the putts didn’t want to drop,” he said.
It was none-the-less a good result for Kruger, who had made $30,000 on the 2015 Asian Tour prior to this week. On Sunday he rose to 25th on the Order of Merit after walking away with a cheque for $110,000.
“I’m playing a lot better now. As soon as I get the putter going, I’ll start to win again. I’m going home, playing next week. Almost on form now and just need to work on the putter,” he said ahead of the Alfred Dunhill Championship, which starts Thursday.