Mexico City:Pumas lost to Saints 4-2 but won 5-4 on aggregate to reach the Mexican Apertura finals against Atlante on Sunday.
It will be Pumas' first finals since 2004, when they achieved consecutive championships.
Carlos Gonzalez and Ignacio Scocco scored for Pumas, who won the first-leg semifinal 3-0.
Emmanuel Luduena's hat trick kept Saints in contention. Luduena scored in the 13th, 36th and 89th minutes and fellow Argentine Matias Vuoso added a goal in the 75th for Saints, who had topped the regular season standings.
But since the Apertura began in 1996, only two clubs have won the championship after leading the league in the regular season. Pachuca did it twice and Toluca three times.
In the other semifinal, Giancarlo Maldonado's goal allowed Atlante to beat Guadalajara 1-0 on Saturday at Cancun.
The series ended 1-1 and Atlante advanced based on its higher seeding for the playoffs. Atlante was third after the regular season and Chivas sixth.
Maldonado, in his first season in Mexico from Venezuela, scored in the three minute for the Colts, who will play the third finals in their history and first since 1992-93 when they won their second Mexican title.
"This team deserves to be in the final, we should have scored more goals, we were the better team," Atlante coach Jose Guadalupe Cruz said.
The finals will probably be played on Thursday in Mexico City and on Sunday in Cancun. The official schedule will be released on Monday by the Mexican soccer federation.