Wanderers advanced 6-5 on aggregate over Union Espanola, while Palestino thrashed Huachipato 6-1.
The two sides will play-off not for the Apertura title - Universidad Chile won that by topping the table after the first phase of the season - but the chance to join the champions and Colo Colo in the Copa Libertadores.
Emiliano Astorga's Wanderers lost their second and home leg 3-2, after winning the first 90 minutes 4-2.
Wanderers were 6-3 up on aggregate during the second half on Sunday, as Roberto Gutierrez - who also scored in the first leg on Wednesday - equalised for the hosts in Valparaiso before Jorge Luna's penalty early after the interval.
Dagoberto Currimilla had earlier given Espanola hope of a revival with a 16th-minute goal, but they would not strike again until the 82nd minute with the aid of one of their former midfielders Gonzalo Barriga.
A Barriga own goal and a Carlos Salom strike brought Espanola back within a goal of forcing an extra period late on but it was to no avail.
Salom finished with three of Espanola's five goals across the two legs.
Meanwhile, Palestino built on their 3-1 away win in the first leg with a 3-0 rout at home to Huachipato on Sunday.
Alejandro Marquez put Palestino ahead on the day, before a German Lanaro brace in the second half sealed a comprehensive victory.
