"We worked hard, but we're in a little bit of a trend of getting down two or three goals and then having to fight back," said Marlies coach Greg Gilbert, who saw his team trail 3-0 midway through the game before rallying to make it close.
"We were in the game, we had a chance to win, but we didn't capitalize on our chances," he added. "We've got to learn from this and move on."
Forwards Ryan Stone and Tyler Kennedy collected power play markers while Stephen Dixon scored at even-strength for the Penguins in front of 3,178 fans at Ricoh Coliseum.
At the other end of the ice, Penguins goalie Andrew Penner was solid, making 40 saves on 42 shots.
"I thought we battled hard in the second half of the game," said Marlies centre Kris Newbury. "It's just too bad there was such a big goal differential."
With the win, the Penguins improved their record (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.
"I didn't play that good tonight," Racine said. "But they have a good team; they didn't give up too many scoring chances, either."
Wilkes-Barre was 2-for-6 on the power play, while Toronto went 0-for-6 with the man advantage.
Stone gave the Penguins a 1-0 edge at 8:09 of the first period, with Toronto defenceman Brad Brown in the penalty box for hooking. Stone, circling at the side of the Marlies net, one-timed Erik Christensen's bouncing rebound over Racine's right shoulder. Wilkes-Barre had a chance to increase its lead in the middle of the first period during a 72-second, two-man advantage while Marlies defencemen David Cloutier and Brown were serving penalties, but couldn't penetrate Toronto's penalty-killing.
In the second period, Kennedy and Dixon scored less than a minute apart midway through the frame to spot Wilkes-Barre a 3-0 lead, but Marlies wingers Williams and Engelhardt solved Penner late in the period to pull Toronto within 3-2.
"It's been a thing all year, getting down by a couple of goals and having to battle back," Newbury said. "We've got to work on improving that."
While on the power play, Penguins left winger Daniel Carcillo centred a pass from behind the net in front to Kennedy, who one-timed the puck past Racine's glove at 7:47. At 8:27, Dixon drove to the net and beat Racine with a backhander high on the glove side, a shot that Racine should have stopped.
Williams put Toronto on the scoreboard at 14:31 of the second period when he faked a slapshot from the left faceoff circle, cut into the slot and fired a wrist shot past Penner. A little over two minutes later, at 16:35, Engelhardt lifted Colin Murphy's rebound over Penner to make it 3-2.
But Penner stepped up in the final frame, making 10 saves to blank the Marlies and preserve the victory. Marlies defenceman Jamie Sifers hit the post with about seven minutes remaining in the third period, but that was as close as Toronto would come.
The Marlies are off until Friday, when they travel to Houston
to play the Aeros.
Notes: Toronto forwards Brad Leeb and John Mitchell and defenceman Carlo Colaiacovo each sat out their third consecutive game with an injury.