The footballer, who played for Rio de Janeiro's Flamengo team, was also charged with kidnapping, hiding a body, forming a criminal gang and corrupting minors, police in the state of Minas Gerais told a media conference.
Even though the body of the alleged victim, 25-year-old Eliza Samudio, has not been found, police wrapping up an initial phase of their probe on Thursday determined that Souza masterminded her death.
"Forensic police will prove that Eliza is dead," the officer in charge of the investigation, Edson Moreira, was quoted, as saying, according to The Telegraph.
Seven other people, including an ex-policeman suspected of carrying out the premeditated murder on Souza's orders, have also been charged. Souza's wife was one among them.
Samudio had been missing for over a month. Police had earlier reported that Souza had met Samudio, at a teammate's party last year and got her pregnant the first night they spent together.
The woman, who had a four-month-old baby called Bruninho (Little Bruno) she claimed was fathered by Souza, was believed to have been demanding child support. The baby was found in the care of Souza's wife.
Souza was suspended from Flamengo, Brazil's most popular club, which he once captained when the allegations against him was first reported.
He was also said to be in talks with AC Milan for his move to the Italian giants before this issue surfaced.