Spain goalkeeper Cata Coll saved the first penalty from Catalina Usme, and Liana Salazar’s went off target, which allowed Aita Bonmati to wrap up matters in the shoot-out in Lyon.
It was a lucky escape for Spain after Irene Paredes, levelled unmarked for them at 2-2 in the seventh minute of stoppage time. Jenni Hermoso had pulled the first back in the 79th after Colombia failed to clear a cross.
Mayra Ramirez had opened the scoring for Colombia in the 12th minute alone in front of Coll, and they seemed on course towards a huge upset when Leicy Santos fired into the left corner for 2-0 in the 52nd, after Coll had saved an initial effort from Linda Caicedo.
Earlier, the US team needed extra time to beat Japan 1-0 at the Parc des Princes in Paris.
The US dominated possession, but it took until minute 105+2 until Trinity Rodman, the daughter of former NBA basketball great Dennis Rodman, fired a superb winner into the top left corner.