The Ecuadorian winger found the net twice as Los Tuzos seized the initiative in a lively first leg.
Carlos Pena scored a header in the 34th minute to put the home side ahead, but the lead didn't last for long.
The reigning champions were brought back to level terms by Enner Valencia's 42nd-minute goal, and pushed into the rearview mirror by his second shortly after the hour mark.
Teenager Hirving Lozano made it three in the 69th minute, and it looked like Pachuca might put itself in commanding position.
But an own goal in the 77th minute - Miguel Herrera jumping for a header and sending it past goalkeeper Oscar Perez - ensured Leon would go into the final with a fighting chance.
Fans of Rafa Marquez making a fool of himself will have been entertained by the Mexico captain's ability to talk himself into a red card in the dying minutes, but it will not please El Tri fans hoping for maturity from their side's skipper ahead of the World Cup.