Toronto is now 2-0-2 under interim head coach Javier Perez.
Chicago is winless in its past three matches.
Yeferson Soteldo gave Toronto a 1-0 lead in the second minute, using his speed to get to the ball at the top left of the goalmouth, sending it to the far post when goalkeeper Bobby Shuttleworth came to Soteldo to try to play the ball.
Chicago had its opportunities to equalize in the first half, with eight of its 15 shots missing the target while Bono stopped all seven shots directed his way.
In the 32nd minute, a one-touch from Boris Sekulic to Robert Beric right in front rolled just wide left. Three minutes later, Beric directed a rocket on goal but Bono denied him with a diving stop. Midfielder Gaston Giminez's shot from just outside the box went wide right in the 37th minute and in the 43rd minute, Bono got his hands on a shot from forward Ignacio Aliseda to deflect it away.
Chicago continued to push for the tying marker in the second half but Bono was up to the task.
There was a save in the 55th minute on Aliseda's shot off a long ball pass. In the 61st minute, Bono jumped to get his hands on a Giminez long-distance shot and four minutes later, Bono went to the air again to snare a header from Chinonso Offor.
Offor came within inches of the tying goal from inside the goalmouth in the 73rd minute but was once again held at bay by Bono. It was the keeper's ninth save of the match, setting a career high.
Midfielder Nick DeLeon went far post from the right wing to put Toronto ahead 2-0 in the 76th minute.
But the home side cut the deficit in half a minute later, courtesy of Alvaro Medran.
Bono continued to frustrate Chicago's attack, getting his hands on Offor's header in the 82nd to keep the visitors in front.