The 62-year-old Autuori replaced ex-Bulgaria coach Dimitar Dimitrov in June.
"Ludogorets's management decided to meet the request of head coach Paulo Autuori to terminate his contract with the club by mutual agreement," the club said in a statement.
Autuori, who guided Cruzeiro and Sao Paulo to Copa Libertadores titles and also managed top Brazilian clubs like Santos, Flamengo and Botafogo, will be in charge for the final time against Bulgarian league leaders Levski Sofia on Oct. 20, the statement added.
Autuori will be replaced by his assistant Antoni Zdravkov, said the club, who have won 11 domestic trophies, including two Bulgarian Cups and two Supercups, since 2011 when they were promoted to the top-flight for the first time.
The 54-year-old Zdravkov, who has also managed Bulgaria's under-21 team, will make his debut as Ludogorets coach against Cyprus's AEK Larnaka in the Europa League on Oct. 25.
Ludogorets failed to reach the Champions League group stages after losing their second qualifying round clash against Hungary's MOL Vidi 1-0 on aggregate. They also lost their first two matches in the Europa League group.
The club said long-serving sporting director Metodi Tomanov has also been released.
(With inputs from agencies.)