It's only the federal elections that use paper ballots counted by hand.
>Dominion provides optical scan paper ballot tabulation systems for provincial elections, including Ontario and New Brunswick. Dominion also provides ballot tabulation and voting systems for Canada's major party leadership elections, including the Liberal Party of Canada, the Conservative Party of Canada, and the PC Party of Ontario.
So Justin Trudeau's election to the leadership of the Liberal Party was indeed accomplished through the use of Dominion voting machines.