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Despite finishing nearly 30 seconds behind Cam Ferguson, Stratford took the title with a convincing two-point lead with his score of 61.835.
He is the first South Island shearer to win the Otago competition's open title in more than 12 years.
Stratford said he was ''feeling great'' about the win and described it as unexpected.
The Invercargill man has been shearing for 17 years, and said he enjoyed meeting a range of people through the sport.
Otago Shearing and New Zealand Woolhandling Championships president Bruce Walker said the open shearing final was one of the best he had seen for several years.
''It was very close, a great win for Nathan [Stratford]. But also good for Otago to have a southern winner after so long.''
The two-day event in Balclutha attracted about 150 competitors which was slightly down from previous years, he said.
Omakau woman Anne-Maree Kahukura won the national senior woolhandling title, after winning the junior title in Masterton last year.
Stratford and John Kirkpatrick represented New Zealand against Wales in the second Elders Primary Wool Shearing Series. Each team had two shearers, and each shore six sheep.
New Zealand won the test, and the final match will take place in two weeks at the Pahiatua Shears.
Open shearing: Nathan Stratford (Invercargill), 61.835pts, 1; Cam Ferguson (Waipawa), 63.903, 2; John Kirkpatrick (Napier), 63.939, 3; David Fagan (Te Kuiti), 65.875, 4; Darin Forde (Winton), 66.738, 5. Senior shearing: Brett Roberts (Mataura), 55.128 points, 1; Cory Palmer (Dipton), 58.340, 2; Brook Todd (Dipton), 58.565, 3; Rob Mainland (Invercargill), 58.978, 4; Jack Fagan (Te Kuiti), 59.278, 5. New Zealand open woolhandler: Pagan Rimene (Masterton), 131.874 points, 1; Joel Henare (Gisborne), 138.500, 2; Tia Potae (Milton), 140.894, 3; Taiwha Nelson (Alexandra), 273.850, 4. New Zealand senior woolhandler: Anne-Maree Kahukura (Omakau), 176.244, 1; Stevie Mason-Smallman (Taihape), 177.220, 2; Ataneta Puna (Napier), 222.618, 3; Juliette Lyon (Alexandra), 234.720, 4. New Zealand woolpressing team: Gordon family, 1; Ken Payne and Bruce Walker, 2; Simon and Corey, 3; Telford boys, 4. Open woolhandling circuit: Pagan Rimene (Masterton), 1; Joel Henare (Gisborne), 2; Keryn Herbert (Te Awamutu), 3; Tina Rimene (Masterton), 4; Amy Ruki (Invercargill), 5; Taiwha Nelson (Alexandra), 6. Shearing and woolhandling team: Dion Morrell team, 127.656, 1; Pango Me Whero, 130.200, 2; A-Bro Hulks, 132.787, 3; Handpieces Hustlers, 153.165, 4.