The 19-year-old French Open winner fulfilled his dream of playing the 35-year-old Agassi and made the most of his opportunity in a final lasting one hour and 58 minutes.
"Agassi is a great player," said the winner, who fell to his knees in joy in victory. "He had a little bit of bad luck today."
Agassi joked that he was glad to have played the youngster "before you retire."
It was Nadal's third title in a row after Bastad and Stuttgart last month.
Nadal's success matched the victory record set by Mats Wilander, who also won nine titles in 1983 as a teenager.
The Spaniard added his first career hardcourt crown to Masters Series trophies this year on clay in Monte Carlo and Rome.
The winner improved to 10-2 in career finals, his only two defeats occurring on cement in Auckland in 2004 and at the Miami Masters when he lost in five sets last March to Roger Federer.
Agassi, seeking a 61st career trophy after winning his last event in Los Angeles, lost a final for the first time in Canada to leave his record in title matches here at 3-1.
Nadal secured a first-set break of Agassi, an eight-time grand slam champion, in the fourth game before the veteran saved a set point to hang on for 3-5.
But a game later, the Spaniard sent Agassi wide on a return, which landed wide to end the set after 40 minutes.
Light rain then forced the pair off court for 58 minutes, with Agassi returning to level at a set apiece before losing in the third on two breaks.
Nadal has won 65 matches this season including the last 16. He lost serve only twice on the way to the Montreal title.
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