The head of the French Football Federation confirmed the coach's departure was based on the Under-21 side's failure to qualify for Euro 2013
The 57-year-old was sacked on Thursday after his side failed to qualify for the finals of Euro 2013, following their 5-4 aggregate defeat to Norway in the play-off round.
There were suggestions that Mombaerts had been removed from his post as a direct result of his failure to discipline five players, including Yann M'Vila and Mbaye Niang, who were spotted in a nightclub after their first-leg victory in Paris, but Le Graet has stressed this is not the case.
He told French radio station RMC: "His [Mombaerts'] resignation has nothing to do with it [the scandal]. We met yesterday (Wednesday). In sporting terms the goal was not reached, so it is logical.
"We know each other well. He came to see me, and we took the decision together."
On the topic of why France's Under-21 campaign came to such a disappointing end, Le Graet said: "You should ask the players, some of whom have already been severely punished. It is very difficult to analyse.
"Consistency of certain players is truly incompatible with the very highest level. But I do not mention names. The investigation is ongoing and we will then make final decisions."
The France chief confirmed he had learned of the unauthorised night out involving M'Vila, Niang, Antoine Griezmann, Chris Mavinga and Wissam Ben Yedder the day after their second-leg defeat, and echoed the growing condemnation of the players from the likes of Guy Roux.
"I learned on Wednesday night, with confirmation this morning (Thursday)," he continued.
"We know the names of players who were out. There was an investigation.
"We are always angry when young players do not respect the rules they themselves have chosen and affirmed. But the federation will investigate very specifically and there will be answers quickly.
"Authorised commissions shall settle for sanctions depending on the severity of the case."
The 71-year-old also stressed that it was not important how the five players were caught, adding: "The rumour reached the federation yesterday, but I do not have precise confirmation how.
"But this is not important. I feel that nobody knew. They made a mistake."