Mangubat held his own against the speedy Thai champion, scoring heavily on left hooks to the body and head. But Wonjongkam, who snatched the crown from another Filipino Malcolm Tunacao in less than a round in Pichit town two years ago, countered with solid blows to earn the nod of the judges.
Jae Bong Kim (Korea), scored it 119-100, Roy O Valle (US), 118-109, and Takeaki Kanaya, 118-109, all for the reigning champion.
Two-time world flyweight champion Erbito Salavarria, the man who called the shots in Mangubats corner, thought the figures were outrageous.
"Kitang-kita naman nila na dumaan sa butas ng karayom si Pongsaklek," said Salavarria. "Hindi naging madali ang laban para sa Thai champion. Maganda ang mga patama natin."
Mangubats manager Yuki Murayama meekly accepted the verdict.
Mangubat wept as he stepped down the ring, but he was widely applauded by the Thai people as he walked back to his dressing area.
Kim only gave Mangubat the 10th round, O Valle picked the Filipino southpaw in the seventh and eighth while Kanaya voted for Mangubat in the seventh and 11th rounds.
Referee Brian McMahon (Australia) even slapped a one-point deduction on Mangubat for holding in the 10th round.