Florida defensive coordinator Randy Shannon was reportedly promoted to interim head coach.
The school also said the "two parties are now negotiating terms of separation".
Controversy surrounded the coach even before the game, though.
The Florida Gators have parted ways with football coach Jim McElwain after a freaky week in which he told the media he was getting death threats - and then lost to rival Georgia by 35 points. An official announcement is expected later in the day.
"We want to thank Coach McElwain for his efforts in leading the Gator football program", said athletic director Scott Stricklin. Mullen also is familiar with the pressure of coaching in the SEC and in Gainesville.
His already-strained rapport with administrators reached a new low last Monday when he said Florida players and families had received death threats.
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Firing him for cause would allow Florida to avoid paying McElwain's buyout, which is in the $12.9 million range.
The Gators are 3-4 overall this year and 3-3 in the SEC, including Saturday's 42-7 loss to Georgia.
The organization hired McElwain in December 2014.
However, McElwain won division titles in his first two seasons with Florida, becoming the first coach to do so since the conference went to a title-game format, and he was named the 2015 SEC coach of the year.
Speculation on McElwain's successor includes Iowa State coach Matt Campbell, Mississippi State coach Dan Mullen (the offensive coordinator for the Gators when they won two national championships in 2006 and 2008), Memphis coach Mike Norvell, Purdue coach Jeff Brohm and SMU coach Chad Morris.
McElwain was 22-12 at Florida, including 16-6 in SEC play.