Jay Heaps' side, who were already assured of their place in the playoffs, head into the knockout stages on a high after Lee Nguyen's first-half goal was enough to down the Canadians.
It was Toronto who started the brighter of both sides and the visitors came within the width of the crossbar from moving ahead after just nine minutes. Gilberto brought a touch of Brazilian flair to the encounter, but saw his overhead cannon off the woodwork.
The hosts did move ahead on 36 minutes, however, as Nguyen collected a pass from Chris Tierney before stroking home from close range to give his side a slender lead at the break.
Both sides cancelled each other out for large periods of the second half, but Luke Moore should have levelled up on 75 minutes after guiding a free header over Shuttleworth's bar.
It proved as close as the visitors would come to restoring parity as Heaps' side held on to finish off their regular season with a win.