Nadal beat unseeded Stefanos Tsitsipas 6-2, 7-6 (7-4) in the final in Toronto on Sunday.
Tsitsipas had produced a stunning run to reach the final – knocking out three top-10 seeds in Dominic Thiem, Novak Djokovic and Alexander Zverev.
The Greek even had a set point to take the match to a third set, but Nadal, after looking shaky towards the end of the second, won the tie-break.
Nadal, the world No 1, took his career haul of Masters titles to 33.
In doing so, he became the first player to book his spot at the year-ending ATP World Tour finals in London.
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And after securing his 80th ATP Tour title, Nadal revealed he wished he had played more in Toronto.
“There have been many years without coming back to Toronto and I miss this tournament a lot,” Nadal said after being presented with the trophy.
“I have had too many injuries in my career to come here more often, but this week has been fantastic.
“To receive this trophy means everything to me.
“And to have the support of you for the whole week means I wake up every morning and try practising every day on court with the highest amount of passion possible.
“Thank you very much.
“Many thanks for all my special memories on court.”
Nadal has now lifted the Canadian Open for the fourth time in his career.
He has been given a bye for the first round of the Cincinnati Masters which begins on Monday.