The ex-Formula One driver finished seventh for Audi Sport, in a race won by Frenchman Jean-Eric Vergne, to end with 181 points.
He became his country's second champion in the electric series after Nelson Piquet, who won the inaugural 2014-15 title.
Outgoing champion Buemi, who had been 10 points clear before coming to Montreal, was runner-up with 157 points after a nightmare weekend.
The Swiss, who had to miss two races in New York due to World Endurance Championship commitments, was disqualified from race one on Saturday for an underweight car. He was then caught in a first corner collision on Sunday before finishing 13th.
His Renault e.dams team did take the team title for the third time in a row, however.
Di Grassi, who won only two races to Buemi's six, was tearful at the finish after a dream come true. He had finished third in the first Formula E season and second in the next.
"After two close seasons we finally made it," he said. "I'm so proud of my team and myself."
Reporting by Alan Baldwin