Ronaldo Koeman’s side secured qualification for next summer’s tournament with a draw against Northern Ireland.
And Van Dijk will play no role in their final Group C fixture on Tuesday.
The Dutch FA announced their captain has now left the squad due to “personal circumstances”.
Van Dijk follows Liverpool teammates Jordan Henderson and Joe Gomez in pulling out ahead of their national team’s final qualifying fixture, with the pair not available for England’s clash with Kosovo.
Mohamed Salah and Andy Robertson withdrew from the Egypt and Scotland squads before the international break.
Liverpool visit Crystal Palace next Saturday before a midweek Champions League meeting with Napoli.
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