Brett Engelhardt and Domenic D'Amour also scored for Toronto (26-34-2-4), which has won three of its last four games.
Stefan Meyer replied for the Americans (38-26-1-0), who have dropped two straight.
Playing before an announced crowd of 3,830, the Marlies opened the scoring with Engelhardt's 20th goal of the season at 6:39 of the first. But Meyer's power-play goal at 15:36 tied the score 1-1.
Toronto regained the lead when D'Amour's shot from the point on the power play eluded Rochester goalie Adam Berkhoel at 12:46 of the second.
The Marlies made it 3-1 just 27 seconds into the third on Sagat's second goal of the year. Sagat rounded out the scoring at 14:46.
Both teams were 1-for-5 with the man advantage.
Marlies goalie Justin Pogge made 31 saves to improve to 14-21-1 while Berkhoel (1-3-0) stopped 23 shots.