Ibrahim Afellay and Gregory van der Wiel were also missing when a 23-strong squad was announced by coach Louis Van Gaal.
"Those four are all changing clubs at the moment and above that they haven't played regularly and are not fit enough", Van Gaal said.
"For them, it is better that they make a fresh start at their new club but the door to my squad stays open because they are good, experienced players."
Van der Vaart was poised to join De Jong in leaving the Premier League on Friday. He had reportedly travelled to Hamburg for a medical, while AC Milan confirmed they had signed De Jong from Manchester City.
Afellay joined Schalke on a one-year loan from Barcelona and Van der Wiel was also expected to move before the transfer window closed at 2200 GMT on Friday.
Van Gaal said the absence of Van der Vaart and De Jong had nothing to do with their performances in the 4-2 defeat by Belgium, his first friendly match since taking charge of the Netherlands for a second time.
Van der Vaart struggled to make any impression while De Jong's second-half blunder initiated Belgium's comeback.
Van Gaal added the changes would not tempt him to play Robin van Persie as a playmaker.
"In the profile I made I consider Robin (van Persie) as a central striker and not as playmaker," Van Gaal said.
Since becoming coach after Euro 2012, where the Dutch lost all three group games, Van Gaal has now introduced nine new players, seven of whom played recently for the country at the under-23 level.
The Netherlands begin their World Cup qualifying campaign on September 7 in Amsterdam against Turkey before they travel to Hungary four days later. Romania, Andorra and Estonia are also in their group.
Goalkeepers: Maarten Stekelenburg ( Roma), Tim Krul (Newcastle United), Michel Vorm (Swansea City)
Defenders: John Heitinga (Everton), Bruno Martins Indi (Feyenoord), Joris Mathijsen (Feyenoord), Ricardo van Rhijn (Ajax), Nick Viergever (AZ Alkmaar), Jetro Willems (PSV Eindhoven), Darryl Janmaat (Feyenoord), Ron Vlaar (Aston Villa)
Midfielders: Urby Emanuelson (AC Milan), Wesley Sneijder (Internazionale), Kevin Strootman (PSV Eindhoven), Jordy Clasie (Feyenoord), Leroy Fer (Twente)
Forwards: Bas Dost (Wolfsburg), Klaas Jan Huntelaar (Schalke), Dirk Kuyt (Fenerbahce), Jeremain Lens (PSV Eindhoven), Luciano Narsingh (PSV Eindhoven), Robin van Persie (Manchester United), Arjen Robben (Bayern Münich)