The province's 2012 offshore wind moratorium blocked the company's 300MW Wolfe Island Shoals project in Lake Ontario, despite agreeing a feed-in tariff (FIT) contract.
It filed a C$475 million (US$356 million) claim for damages under the North American Free Trade Agreement (NAFTA) in the same year.
A NAFTA tribunal partially ruled in Windstream's favour, awarding about C$25 million in damages and C$3 million legal costs.
The payment made to Windstream includes roughly C$240,000 in interest, according to a The Canadian Press report, which accrued after the government failed to meet an October 2016 deadline.
The FIT contract for Wolfe Island Shoals remains in force, but Ontario's offshore wind moratorium remains in place, leaving the future of the project unclear.
Ontario energy minister Glenn Thibeault said the decision to place a moratorium on offshore wind is "one our government still believes is correct" despite the NAFTA award.
The province has said it wants to see how the proposed 20.7MW Icebreaker project on the Ohio side of Lake Erie goes before deciding whether to proceed with development in Ontario waters.