Van Persie has scored three of the Netherlands' 12 goals at the tournament, although he has not found the net in their last three games.
"He has some stomach problems, some intestinal problems, so it's best not to train him," Van Gaal told reporters at the Corinthians arena on Tuesday.
The 30-year-old started the tournament with a bang, scoring twice against Spain including a diving header which is a candidate for goal of the tournament. He scored against Australia but picked up a second yellow card, ruling him out of the Netherlands' final group game against Chile.
Van Persie was substituted late on against Mexico in the last 16 and his replacement Klaas-Jan Huntelaar scored the winner from the penalty spot in stoppage time as the Dutch battled back from a goal down.
In the quarter-final against Costa Rica, Van Persie missed a series of chances but scored the Netherlands' first penalty in a shootout victory that sealed their place in the semi-finals.
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