Forwards Ryan Stone and Tyler Kennedy collected power-play markers, while Stephen Dixon scored at even-strength for the Penguins.
The Penguins improved their record to 8-1-0 to remain in first place in the Eastern Conference, and are a perfect 5-0-0 on the road this season.
Forwards Jeremy Williams and Brett Engelhardt provided the scoring for the Marlies, who fall to 4-5-1.
Toronto goalie Jean-Francois Racine made 34 saves on 37 shots.
Wilkes-Barre was 2-for-6 on the power play, while Toronto went 0-for-6 with the man advantage.
The Marlies are off until Friday, when they travel to Houston to play the Aeros.