Chicago (14-8-5) won for the fifth time in six matches and moved past both Houston and New York into second place in the Eastern Conference with 47 points -- three behind front-running Kansas City.
Pavel Pardo set up Chicago's first score by hitting the post and grabbing his own rebound. Pardo's cross was then headed home by Fernandez.
Rolfe scored just before halftime after Toronto failed to properly clear the ball.
Eric Hassli produced Toronto's goal in the 79th minute. Toronto (5-17-6), winless in eight straight outings, is in last place in the East.