France lost their play-off against Norway 6-3 on aggregate after a shambolic second leg performance, which they lost 5-3 despite being clear favourites.
Mombaerts, who has been in the job since 2008, has now failed to qualify for all three European U21 Championships in that period.
"The French Football Federation president and U21 national coach met on Thursday morning,” the FFF said in a statement.
"Following their exchange and by mutual consent, Erick Mombaerts will no longer continue as head of the U21 team. Erick Mombaerts remains on the national coaching staff."
France had won seven of their eight Group 9 matches to reach the play-offs, which all group winning-sides must contest to qualify for the finals.
They also lost a play-off to eventual winners Germany in 2008, and failed to get out of their group in 2010.
Mombaerts, 57, was widely criticised for failing to discipline several players who went out on Saturday night, between their first and second legs play-off matches.
France had won the home leg 1-0 but slumped to a 5-3 defeat in Norway on Tuesday, meaning they will not contest the finals in Israel next year.
Yann Mvila, Antoine Griezmann, Chris Mavinga, Mbaye Niang and Wissam Ben Yedder were all spotted in a nightclub on Paris’ Champs-Elysees, which was backed up by photographs on social networking sites.
It is understood that, on Saturday night, they left by taxi from the national team’s training camp in Le Havre, where their first leg had been played, and did not return until the early hours of Sunday morning.
Mombaerts is reported to have spoken to the players but decided not to punish them.
Rennes, meanwhile, are set to discipline their players who were involved in the night out, Mvila and Mavinga, a lead that other French clubs are expected to follow.
“We deplore this affair,” Rennes general manager Pierre Dreossi said. “I will summon these players on Friday for a frank discussion.
“I still don’t know the full facts, but if it is found to be true we will contact the French Federation and will agree to any decisions we make together.”