Brazil's soccer federation (CBF) announced Antony's withdrawal on Monday after local media outlet UOL published allegations of physical assault against him from ex-girlfriend Gabriela Cavallin.
The player has denied wrongdoing.
The English Premier League club had been under pressure to respond to the allegations against Antony in the wake of a decision to part company with another striker, Mason Greenwood (21).
Manchester United said last month that Greenwood would leave Old Trafford to avoid being a "distraction" after he had faced allegations of assault and attempted rape.
Those charges were dropped in February, said prosecutors, citing "the withdrawal of key witnesses and new material that came to light". Greenwood last Friday joined Spanish LaLiga side Getafe on a season-long loan.
Manchester United said it took the case against Antony seriously, "with consideration of the impact these allegations and subsequent reporting will have on survivors of abuse."
The club said they acknowledged the police inquiry and would make no further comments on the issue pending further information.
The Brazilian federation said Antony was being pulled from the squad "in order to protect the alleged victim, the player, the Brazilian national team and the CBF."
Antony said he could give no more details about the allegations due to the police investigation, but that he could "confidently state" that they were false.
A spokesperson for Brazil's Public Security Secretariat confirmed to Reuters that a police investigation was underway.