Romanian Halep's shaky serving from her semi-final win the day before carried over at the outset of the final as she produced four double faults and was broken in the opening game.
Halep responded by changing her tactics, drawing the Brazilian into longer rallies to reel off six straight games and sealed the opening set when she blasted a forehand winner, pumping her fist as the supportive crowd roared their approval.
Haddad Maia dominated the second set but got tight in the decider, badly missing a forehand wide to hand Halep a 4-1 lead that she would not relinquish.
The two-time Grand Slam champion sealed her ninth WTA 1000 title when Haddad Maia's service return found the net on match point under sunny skies in the Canadian city.
"At the start it was really tough," Halep told reporters.
"She's lefty, so it's coming different, the spin. She's very powerful. She's solid. And it's never easy to play against her."
With the win, the former world number one will re-enter the top 10 next week at number six.
"I've been many years there but now I feel like it's a big deal to be back in top 10. I'm really happy with this performance," she said.
"When I started the year I was not very confident and I set the goal to be, at the end of the year, top 10. And here I am. So it's very special moment.
"I will enjoy it. I will give myself credit. I'm just dreaming for more."
The loss ended an impressive run at the tournament for Haddad Maia, who toppled local favourite Leylah Fernandez (19), world number one Iga Swiatek (21) and Tokyo Olympics gold medalist Belinda Bencic (25) en route to the final.
"I think I'm getting more competitive every week and we are working the right way," Haddad Maia said.
"The results are here because we are focused on the process."
Haddad Maia will debut in the top 20 for the first time next week and her success caught the attention of Brazilian soccer hero Pele.
"How good is it to see Brazilians conquering more and more in the sport," Pele posted on social media ahead of the match.
"I want to congratulate Bia for reaching the Toronto WTA 1000 final, but above that, for the beautiful journey so far."
