Favre returned to the Ligue 1 club for a second stint in charge in June 2022 as it invested ahead of the new season.
The former Borussia Dortmund boss had guided Nice to Champions League qualification in 2016-2017, but his latest spell did not yield the same success.
Despite making a series of high-profile signings, including Aaron Ramsey, Ross Barkley and Kasper Schmeichel, Nice is in 11th in Ligue 1.
The final straw for Favre was Sunday's (AEDT) cup elimination at the hands of lower-league opposition, with Nice winless since the World Cup break.
Didier Digard will take charge of Nice "until further notice", with a Ligue 1 double-header against Montpellier and Reims this week.
"As the two parties now go their separate ways, everyone at the club would like to show him the utmost respect, as he will remain a special member of the Rouge et Noir family, with the 2016-17 season having left an indelible mark in the hearts of Le Gym fans everywhere," A Nice statement read.
Favre became the second Ligue 1 coach to be removed from his post on Tuesday (AEDT), after Julien Stephan's dismissal at Strasbourg.