Poor results in off-season friendlies and the first four matches of the domestic Apertura championship and defeat by Brazil's Internacional in the South American Supercup last month did not help Mohamed's cause.
"I'm not taking this decision, the barra bravas took it," said Mohamed, using the term for gangs of hooligan fans who blight Argentine football, after saying farewell to the players at Independiente's training grounds.
About 200 Independiente barra bravas chanted insults at the players and Mohamed outside the changing rooms at the Libertadores de America stadium after Sunday's night's defeat, calling for them to go. As the team left the ground they played a funeral dirge.
"Ninety percent of the fans did not insult [us during the match] and have always backed... the players and coaching staff. Yesterday, a group of barra bravas, sent or not sent [to do this], went to insult us and left a very clear message," Mohamed told reporters.
There have been reports of a relationship between barrabravas and club directors for years with the latter financing trips to away matches and even abroad. Sources close to the club said Mohamed had refused to give in to barrabravas' demands for money.
Mohamed, a former Argentina striker who had been in charge for 11 months, steered Independiente to victory in last year's Copa Sudamericana, South America's Europa League equivalent, leaves with a record of 16 wins and 16 defeats in 51 matches.
"The club were international champions, will play the next Sudamericana, are three points from qualifying for the Copa Libertadores... this wasn't a sporting issue," Mohamed said.
"Argentine football is in a bad state," added Mohamed, whose place will be taken for the time being by caretaker Christian Diaz, a junior team coach.
Independiente are the record seven times South American champions but the last time they won the Copa Libertadores was in 1984. They have 14 domestic league titles but only two in the era of two championships per season which began 20 years ago.
