After race one of the Indy Toronto was postponed on Saturday due to adverse weather conditions, Bourdais was a clear winner when the action finally got under way 24 hours later.
The Frenchman, driving for KVSH Racing, won by a margin of 3.3 seconds ahead of series leader Helio Castroneves (Team Penske) - ending a seven-year wait since his last race victory.
Bourdais could have triumphed by a greater margin but was hindered when he hit traffic in the closing stages and also had to overcome a scare when he hit part of the suspension that fallen off the car of Ryan Hunter-Reay (Andretti Motorsport).
However, he did enough to claim his 32nd career IndyCar victory and his first since 2007.
Hunter-Reay was involved in a collision with Tony Kanaan (Chip Ganassi Racing) during their battle for third. The clash was deemed to be a racing incident but while Kanaan recovered to take the final spot on the podium, Hunter-Reay's car suffered too much damage and his race was over.
Simon Pagenaud (Sam Schmidt Motorsports) had to fight his way through the field to finish fourth after an early collision with Luca Filippi (Rahal Letterman Lanigan Racing) left him at the back of the field, while Scott Dixon (Chip Ganassi Racing) rounded off the top five.
Race two of the weekend will take place later on Sunday.