Smeets, who is ranked No. 438 in the world, was ahead, 3-1, in the third frame when he was slowed down by cramps in the left leg. This gave the world No. 42 Kwon the opportunity to take the next two games at 4-3.
But Smeets, determined to win his first ITF title, braved the pain. He broke Kwons serve at 4-4 and took the next two games to win the 2 hours, 10-minute match.
"We ran around. Im very tired. I lost a lot of energy," said the 16-year-old netter from Ipswich, who became only the second Australian champion after Lleyton Hewitt won in 1997.
"When I got the cramps, I tried to run around and it went away. When I reached the finals yesterday, I was happy. Now Im very, very happy," said Smeets, who ousted No. 2 Michel Koning of the Netherlands in the first round and No. 4 Liu Tai-wei of Chinese Taipei in the semifinals.
Smeets, who reached the second round of the Australian Open Juniors last January, promised to defend his title next year.
"This is an important win for me. Definitely, I will be back here in Manila to defend my title," said Smeets, who earned 100 ITF Juniors points in this event presented by Adidas and supported by Wilson balls, Manila Midtown Hotel, Viva Mineral Water, Pioneer, 3M and the Philippine Sports Commission.
In the girls singles finals, top seed Taiwanese Hsieh Su wei defeated compatriot No. 8 Chan Chin-wei, 6-1, 6-3, to retain the title.
Hsieh and Chan won the doubles title over Australian pair Bubravka Cupac and Daniella Dominikov, 6-2, 1-6, 6-4.
Top seeds Michel Koning and Bas Van Der Valk of the Netherlands pocketed the mens doubles title over third seeds Adam Feeney and Christopher Guccione of Australia, 6-3, 7-5.