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Assistant coach Steve Komphela would take charge of South Africa's next two matches.
"Both parties [Mosimane and SAFA] agreed to part ways amicably in the best interests of both the country and the national team," SAFA said in a statement.
Bafana drew 1-1 against unfancied Ethiopia in their opening match of the 2014 Soccer World Cup qualifiers in Phokeng, outside Rustenburg, on Sunday.
They face Botswana in another crucial qualifying fixture in Gaborone on Saturday, and they play Gabon in an international friendly in Johannesburg later this month.
Mosimane, 47, signed a four-year contract in July 2010, replacing Brazilian Carlos Alberto Parreira shortly after the national team was eliminated in the first round of the World Cup in South Africa.
He got off to a superb start, guiding Bafana to six victories and only one defeat in his first nine matches in charge.
The wheels started to come off, however, as they began a lengthy dry run, failing to win any of their last seven games as they struggled to find the back of the net.
Of the 16 matches South Africa played with Mosimane at the helm, they won six, drew seven and lost three.
During his shortened tenure, Bafana failed to qualify for this year's Africa Cup of Nations after team management misinterpreted the rules, assuming they needed to draw their last match, a must-win encounter, to reach the continental showpiece,
Moroka Swallows coach Gordon Igesund has been tipped to take over from Mosimane on a permanent basis.
SAFA said caretaker coach Komphela would address the media at the squad's training camp in Phokeng later on Tuesday morning.
Mosimane’s record as Bafana coach:
South Africa 1 Ghana 0 (friendly international - 11/8/2010)
South Africa 2 Niger 0 (2012 Africa Cup of Nations qualifier - 4/9/2010)
Sierra Leone 0 South Africa 0 (2012 Africa Cup of Nations qualifier - 10/10/2010)
South Africa 0 USA 1 (friendly international - 17/11/2010)
South Africa 2 Kenya 0 (friendly international - 9/2/2011)
South Africa 1 Egypt 0 (2012 Africa Cup of Nations qualifier - 26/3/2011)
Tanzania 0 South Africa 1 (friendly international - 14/5/2011)
Egypt 0 South Africa 0 (2012 Africa Cup of Nations qualifier - 5/6/2011)
South Africa 3 Burkina Faso 0 (friendly international - 10/8/2011)
Niger 2 South Africa 1 (2012 Africa Cup of Nations qualifier - 4/9/2011)
South Africa 0 Sierra Leone 0 (2012 Africa Cup of Nations qualifier - 8/10/2011)
South Africa 1 Ivory Coast 1 [friendly international - 12/11/2011)
Zimbabwe 2 South Africa 1 (friendly international - 15/11/2011)
Equatorial Guinea 0 South Africa 0 (friendly international - 6/1/2012)
South Africa 0 Senegal 0 (friendly international - 29/2/2012)
South Africa 1 Ethiopia 1 (World Cup 2014 qualifier - 3/6/2012)
