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The 15-year-old, who was playing in Thailand after winning the ISPS Handa NZ Women's Open and finishing third at the Australian Open in consecutive weeks, had another fine week at the Siam Country Club in Chonburi.
Ko carded rounds of 69, 71, 74 and 69 for a five under par total of 283 to finish seven shots back from the South Korean winner Inbee Park who won by one shot from local hope Ariya Jutanugarn.
The Pinehurst School student made five birdies and two bogeys in her final round that saw her climb five places and once again place near the top of a world-class field.
She kept alive her record of never missing a cut in a professional event and claimed the title for the leading amateur at the event finishing 15 shots ahead of Thailand's Suppamas Sangchan.
Ko will now head to Queenstown to play in the NZ PGA Pro-Am at The Hills where she will play as a celebrity amateur in the tournament that begins on Thursday.
Australian-based Kiwi Michael Long saved his best for last when he carded a six under par 66 in the final round of the Victorian Open to finish in a share of 14th place on the PGA Tour of Australasia.
The New Zealand Open champion of 1996 had rounds of 77, 67, 70 and 66 for an eight under par 280 total to finish five shots back from Australian Matthew Giles who won the title by one shot.
Long made seven birdies and a bogey in his final round that saw him climb from a share of 40th place into the top 15.
Tauranga professional Josh Geary, who began well with a four under par 68, faded to finish on a two under par total and claim a share of 40th place.
Brad Shilton (74, 72), Gareth Paddison (73, 73), David Klein (73, 74), Ryan Fox (72, 75), Kieran Muir (74, 73), Steven Alker (76, 71) and Hamish Robertson (80, 66) all missed the cut.
Pieter Zwart, Phil Tataurangi, Troy Ropiha and Mark Brown were other Kiwis to miss the weekend.
Wellington professional Nick Gillespie opened with a seven under par 65 to lead the event by two shots but was disqualified moments after for not signing his scorecard.
Lee slow to start in Panama
Meantime over on the Web.Com Tour New Zealand No.3 Danny Lee has made a slow start to the season in Panama.
The 22-year-old from Rotorua had rounds of 74 and 71 at the Panama Golf Club in the season opener to miss the cut by three shots.
The former PGA Tour player, who missed his card by one shot in final qualifying last year, needs to finish inside the top 25 players on the Web.Com Tour to return to the game's most lucrative tour.