Chile beat Palestino 4-2 on aggregate after winning their home leg 3-1 on Monday - with Rodrigo Rojas netting a brace.
Iquique beat Universidad Catolica on penalties after their two-legged tie finished 3-3 - with Iquique forcing the shootout courtesy of their 1-1 road draw in the second regulation 90 minutes.
The two sides will now play off for a spot in the continental tournament.
Rojas put Chile ahead on aggregate when he struck in the seventh minute at the Estadio Santa Laura-Universidad SEK in Santiago.
Gustavo Lorenzetti doubled their lead for the match, and extended the overall lead to 3-1 when he got on the scoresheet later in the half.
Palestino's hopes of advancing were bettered by a 56th-minute goal to Roberto Gutierrez, but Rojas' second ended the visitors' chances.
Iquique were on the canvas in their second leg at Catolica's Estadio San Carlos de Apoquindo, as Matias Jadue's goal had the home side bound for the play-off final.
But Manuel Villalobos' equaliser with 12 minutes to play sent the match to a shootout, one which Iquique claimed 3-2.
