Van Gaal pulled Jasper Cillessen in the 120th minute in favour of the slightly taller Tim Krul, who made two saves to help the Dutch reach the semifinals.
"Every player in my selection has certain skills and qualities and they don't always coincide," Van Gaal said. "We always felt that Tim Krul would be the most appropriate player to stop penalties.
"He has a long reach and we prepared Costa Rican penalties. He dove into the right corner time and time again. We are a little bit proud that this trick has helped us through."
The Netherlands staff had discussed the goalkeeper change as they prepared for the match -- but no one told starting keeper Cillessen.
"First and foremost, the coach decides who is going to play and who is going to be a substitute," Van Gaal said. "We said nothing to Jasper Cillessen because we didn't want to face this before the match. It would be disappointing for him, but every keeper has his specific qualities. We felt Tim had a better track record of saving penalties. Fortunately, this worked out."
Krul has saved two of 20 penalties during his time with Newcastle but failed to stop any of the five spot-kicks he faced last season.
The incoming boss of Manchester United said he planned to use Krul while heading into extra time, and didn't feel the move came at the expense of swapping out a third outfield before the shootout.
"Before the 90 minutes had ended, I thought they were playing well and that we created lots of opportunities. I didn't have this need to substitute anyone," Van Gaal said.
"I felt that Memphis [Depay] didn't play really well, so I exchanged him for [Jeremain] Lens. In the extra time, I took into account that I would maybe want to use Krul should it come down to penalties.
"Of course, we also had the injuries to [Ron] Vlaar. [Georginio] Wijnaldum was exhausted, [Robin] van Persie as well. I brought in [Klaas-Jan] Huntelaar, which was a risk. I went from five to four defenders. It was a bit tricky, touch-and-go, but in hindsight, it was a big success."
The Netherlands move on to face Argentina in the semifinals on Wednesday, and Van Gaal was not very complimentary of his next opponents.
"I saw a match today that Argentina was just stopping and slamming on the brakes," Van Gaal said of the Albiceleste's 1-0 victory over Belgium earlier on Saturday.
"I only saw one half of the Argentina match. The beginning was in favor of Argentina and after that, it was Belgium who dominated. I thought Belgium was the better team in the first half. Argentina have strong individual qualities. If the gentleman next to you says Argentina always attacks, well that was not the case against Belgium. Not in the first half."
Van Gaal also said it was a shame that the Netherlands would not be able to face their southern neighbours.
"It's a pity that Belgium have lost," he said. "You must have inferred that from my answers. Well, that's life, isn't it?"
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