Red-hot forward Christian Volesky put the Rhinos up in the first half, but Toronto battled back to equalize off the head of Skylar Thomas.
After Saturday's emphatic come-from-behind 3-1 win at home over FC Montreal, Rochester took a five game unbeaten run up to Ontario to face Toronto FC II.
Toronto had just achieved its first set of back-to-back wins in team history on the weekend and looked to carry on that form against the team it had beaten back on June 11.
Rochester had a shortage of available field players for Wednesday night's game and could only name six players to the bench including third-strong goalkeeper Daniel Lynd.