The Galatasaray forward was not "intact" after the 0-0 weekend draw with Northern Ireland and has returned to his club, according to statement from the Royal Dutch Football Association (KNVB).
Babel, 32, started in Belfast and lasted until the 90th minute before making way for defender Nathan Ake.
Ronald Koeman has now lost three of the players who started Saturday's stalemate, which was enough to confirm the Oranje's qualification for Euro 2020.
Virgil van Dijk was released from the squad for personal reasons, while Martin de Roon is suspended after receiving a third yellow card.
Netherlands are two points behind Group C leaders Germany going into their meeting with bottom-placed Estonia in Amsterdam.
Babel scored twice as Koeman's men ran out 4-0 winners when the teams met in Tallinn in September.