The Belgian's absence is not expected to impact teammate and race leader Jonas Vingegaard, who is on course for a second consecutive title after his rival Tadej Pogacar lost time following a crash in Wednesday's stage 17.
"In consultation with the team, we have decided that my place is now at home," the 28-year-old said, adding that the family's doctor had informed him his wife was expected to go into labour soon.
"I always thought that I would go home when my wife indicated that she needed me. That time has come."
Thursday's stage 18 is a 185km ride from Moutiers to Bourg-en-Bresse.