Noble Okello seemed to give Toronto a lead in the 29th minute with a header but was deemed offside by the side referee.
Patrick Mullins gave Toronto the lead when he tapped in Jacob Shaffelburg's cross atop the six-yard box.
The Canadian club doubled the lead in the 71st minute when Leon goalkeeper Rodolfo Cota contested a ball that deflected off Justin Morrow and into the net.
The Liga MX side pulled one back in the 80th minute when Fernando Navarro pounced on the ball upon making an unmarked run into the 18-yard box.
With Leon pressing in the final moments, Alex Bono made a series-clinching save for Toronto in the 90th minute.
Toronto played as the home side at the ESPN Wide World of Sports complex in Florida due to travel restrictions in Canada.