The visitors took the lead after just seven minutes when Ryan Johnson shot home from distance.
However, Red Bulls restored parity just six minutes later when Markus Holgersson headed home Henry's corner kick.
Kenny Cooper made it 2-1 to the hosts in the 28th minute with a simple tap-in after being teed up by Henry.
The Frenchman was back weaving his magic in the final stages of the encounter at the Red Bull Arena.
The former Arsenal and Barcelona striker set up Cooper for his second goal of the match on 88 minutes, and himself found the target in the third minute of injury time with a chip from outside the Toronto penalty box.