Lee Goren scored the game winner, Brad Moran added his 20th of the season, and J.J. Hunter rounded out the scoring for Manitoba. Justin Pogge blocked 22 shots for Toronto.
With the victory the Moose move into sole possession of first place in the North Division with a 33-17-7-4 record. With 77 points, Manitoba is two ahead of Rochester and three ahead of Hamilton, which lost to Milwaukee 3-2 in a shootout.
The Moose scored the lone goal of the first period at 10:33 when Goren pounced on a Moran rebound, spun around at the front of the crease and backhanded the puck along the ice and between Pogge's pads.
Following a lacklustre opening period, both teams took the body in the middle frame with the Marlies picking up the pace, outshooting the Moose 15-8. But Manitoba, who won the previous four games against Toronto, all at the Ricoh Coliseum, maintained their one goal lead in front of 8,363.
At 2:11 Moran scored unassisted, and staked Manitoba to a 2-0 lead when he corralled the puck behind Toronto's net and deftly backhanded it off the back of Pogge's right leg and into the net.
Flaherty was solid in the second period, especially when Manitoba, which boasts the top penalty-killing unit in the AHL, was under siege.
Ex-Marlie J.J. Hunter added the third marker when he went right in on goal and backhanded the puck over Pogge's shoulder to ensure the victory.
Toronto were 0-8 on the power play, while Manitoba went 0-5.