Kyle Chipchura, with two, Jonathan Ferland, Mikhail Grabokvski and Duncan Milroy scored for the Bulldogs (13-9-0-1), who have beaten the Marlies in three of five attempts this season.
John Mitchell, Brett Engelhardt and Erik Westrum replied for Toronto (9-12-2-2), which dropped its third straight.
The Marlies gave the Bulldogs 10 man advantages during the game, including six straight in the second period. Hamilton only converted on one power play, but constant penalty killing wore the Marlies down.
"That's a frustrating way to lose, when you're killing (penalties for) 13-14 minutes in one period," Engelhardt said after the game. "That's more than most teams do in a game. That's tough to swallow."
Added Marlies coach Greg Gilbert: "You can't take penalties now - that's all the game is. Our discipline has to be better than it is."
Toronto took a 1-0 lead when Mitchell scored his fifth of the year at 4:55 of the first period. The Marlies failed to score on a two-minute, 5-on-3 advantage late in the period, and Hamilton immediately took advantage when both penalized Bulldogs came out of the box and broke in alone on Toronto goalie Jean-Francois Racine.
Ferland scored on the play with just 14 seconds left in the first to pull Hamilton even.
The Bulldogs took their first lead of the night at 12:04 of the second period on Grabovski's power-play goal, but Toronto tied it up 42 seconds later on Engelhardt's eighth of the season.
Milroy jabbed a loose puck past Racine at 18:34 of the second, in a play hotly disputed by Marlies players, to give Hamilton a 3-2 lead.
Westrum's goal at 4:14 of the third evened the score again, but Chipchura put the Bulldogs in front for good at the 9:05 mark. Chipchura also had an empty-net goal with 45 seconds remaining.
"We can't stick with the same game plan for 60 minutes," Gilbert said. "We've proven that time and time again. It's something as a group we're going to have to learn."
Bulldogs goalie Yann Danis (6-5-0) made 37 saves in the loss, while Racine stopped 26 Hamilton shots to fall to 5-5-2 this season.
Notes: The attendance at the game was the worst in Marlies history. The previous low was 2,049, set last Dec. 20 against Lowell…Bulldogs centre Zack Stortini and Marlies winger Tyson Nash were ejected from the game at the end of the second period after a particularly nasty fight. Toronto's staff and players were not impressed by Stortini's excessive actions. "He was kneeing (Nash), he was elbowing him in the back of the head, and he gets two (extra) minutes for that," Gilbert said of Stortini. "It's beyond me."…The Marlies announced that defenceman Michael Schutte would be released from his professional tryout contract Thursday.
Schutte, who signed a PTC with Toronto Oct. 2, had a goal and two points in 11 games with the Marlies this season. He is expected to sign a contract with a German pro team.