The Qatar Football Association said in a statement that they had mutually agreed to end the tenure of Autuori, who replaced fellow Brazilian Sebastiao Lazaroni last February.
With three fixtures remaining, Qatar are in fourth place in Group A of the final Asian qualifying round for the 2014 World Cup, a point behind leaders Uzbekistan, and travel to South Korea on March 23 for their next match.
The top two sides qualify automatically for the finals in Brazil.
QFA president Sheikh Hamad Bin Khalifa Bin Ahmad Al Thani thanked Autuori, who also managed Qatar's Olympic side for five months, for his contribution.
"The decision to appoint Fahad Thani came after close consideration of his coaching credentials, notwithstanding the fact that he has been working closely with the national team for quite some time, as Paulo Autuori's assistant," the president said.
"Moreover, he has intimate knowledge of the national team and Qatari football in general and will be a great addition to our team."
Thani's first task will be to oversee Qatar's opening qualification match for the 2015 Asian Cup at home to Malaysia on February 6.