Dominic Oduro scored the game's only goal as his side continued its recent trend of beating Toronto.
Columbus scored the game's lone strike in the 42nd minute, speedster Dominic Oduro latching on to a long pass from Federico Higuain.
The win puts Columbus into the playoff spots for the time being. Toronto sinks to 1-7-4 on the season, the second-worst record in MLS.
The Crew have won the Trillium Cup four out of five years.