Following a scoreless opening period in which the Senators outshot the Marlies 19-9, the teams combined for seven goals in the second.
Grant Potulny, Jean-Francois David and Heerema - with two - gave Binghamton (11-21-1-2) a 4-3 lead by the second intermission.
Brett Engelhardt scored twice for Toronto (14-17-2-3), with Erik Westrum adding the other Marlies goal.
Still trailing 4-3 with two minutes remaining in regulation, Toronto pulled goalie Jean-Francois Racine for an extra attacker and Colin Murphy tied the match with 35 seconds left on the clock as he chipped a shot over the left shoulder of Senators goalie Kelly Guard.
The Senators won the shootout 3-2 on goals by Ryan Vesce, Danny Bois and Heerema - on his second attempt of the tie-breaker. Erik Westrum and David Cloutier scored for the Marlies.
Racine finished with 43 saves while Guard stopped 31 shots.