Puebla will face Estudiantes Tecos, formerly known as UAG, in the first game at the Home Depot Center. America, the winner of Group A, will face Monterrey in the second game.
The two winners will advance to the 2010 Copa Libertadores.
Gomez, who spent six seasons with three teams in MLS, played the first 71 minutes before giving way to former MLS MVP Carlos Ruiz, who had two goals and an assist in Puebla's earlier wins.
U.S. international Edgar Castillo started for Tigres in Sunday's first game, a 2-2 tie with Jaguares that left both teams with only two points.
Monterrey's win gave it five points, second behind Puebla.
On Saturday, Estudiantes Tecos rallied from 3-1 on goals by Chilean Rodrigo Ruiz and Paraguayan Fredy Bareiro in the second half and earned 3-3 tie with America that was enough to send both teams into the Wednesday's finales.
In the first game, Santos beat Atlante, 3-0, for its first three points of the tournament.