Nick Drazenovic tied the game with 12.9 seconds remaining to force overtime.
Anton Zlobin and Scott Harrington had the other goals for the Penguins (32-20-5), who won for the fourth time in 12 games. With the win, the Penguins improved to 4-3-0 in their last seven against Toronto.
Trevor Smith, Spencer Abbott and Kenny Ryan scored for the Marlies (34-19-5), who lost for the second time in three games this weekend.
Jeff Deslauriers made 31 saves in the win while Toronto's Drew MacIntyre stopped 31 shots.
With their goaltender pulled for an extra attacker, Drazenovic forced overtime by one timing an Ebbett feed past MacIntyre.
Smith gave Toronto its first lead of the game going backhand, top corner on Deslauriers at 15:59 of the third.
Abbott evened it at 2-2 on a power play, beating a screened Deslauriers for his 14th of the season at 10:56 of the third. The goal stretches Abbott's point streak to three games.
Zlobin gave the Penguins their second lead of the game at 18:24 of the second poking home a loose puck for his sixth of the season.
Ryan tied it 1-1 at 3:16, shorthanded, on a partial break, beating Deslauriers blocker-side from the top of the faceoff circle. The goal broke a five-game drought for Ryan.
Jerry D'Amigo extended his point streak to six games with his assist on the goal.
Moments later, Ebbett nearly gave the Penguins their second lead of the game. But with MacIntyre down and out Ebbett's shot hit the post.
The Marlies outshot the Penguins 12-4 at one point of the first period, but had nothing to show for it.
Harrington opened the scoring at 17:59 of the first, beating MacIntyre from the faceoff dot.
The two teams play for a second and final time April 13 at Wilkes-Barre, Pa
Toronto's next game is Friday when the team visits Rochester.
Notes: Marlies LW Jamie Devane missed the game serving a one-game suspension as a result of receiving an instigator penalty during the final five minutes of Saturday's 4-1 win over Lake Erie. Under rule 46.22 both the Marlies and coach Steve Spott were also fined US$500 each. Devane picked up four minor penalties, a major, a misconduct and a game misconduct for 33 minutes in penalties in the win. The suspension is Devane's second this season. He missed one game in November stemming from a boarding incident.