After Leon took the lead at home just after the half-hour mark, Valencia equalised for Pachuca three minutes before the break and then put the visitors ahead in the 61st minute with a strong header.
Pachuca claimed a 3-1 lead with 21 minutes remaining thanks to Hirving Lozano's strike and although an own goal to Miguel Herrera reduced the visitors' advantage, Leon face a tough task to triumph in the two-legged final.
Dieter Villalpando was the star for Pachuca as the 22-year-old midfielder created all three goals for Enrique Meza's side.
As the match ticked into the final half-hour, Valencia and Villalpando combined again, with the former getting ahead of his marker to power the latter's corner into the net from the edge of the six-yard box.
But Leon remain in contention after Herrera nodded Elias Hernandez's free-kick into his own net in the 77th minute.
Leon, who won the Apertura title in December, will travel to Pachuca's Estadio Miguel Hidalgo for the second leg on Sunday.
