Van Persie suffered a groin injury in Holland's friendly win over Wales but both he and Van Gaal insisted the problem was not serious.
Van Gaal said: "He has a little injury and I think it is better that you don't risk a bigger injury when he plays the second half.
"I think he made the right decision. It is not an important match. You don't have to risk it.
"His action to give the assist for the first goal was fantastic."
Asked if Van Persie should be fit for Holland's World Cup opener against Spain on June 13, Van Gaal said: "I hope so, and I think it is so."
Van Persie himself said: "I wouldn't call it an injury, I came off as a precaution.
"It built up during the came so decided it was sensible to come off."
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