In a statement, the festival said it would "present the film as planned".
The film's release plans were cast into doubt after it emerged that a woman who accused director Nate Parker of rape in 1999 later took her own life.
Parker, who also stars in the Oscar-tipped film, was acquitted of raping the woman while at university.
His roommate Jean Celestin, who has a story credit on The Birth of a Nation, was convicted of sexual assault.
The conviction was later overturned when the woman opted not to testify again for a 2005 retrial.
The incident has come back into the press ahead of the US release of Parker's drama about Nat Turner's 1831 slave rebellion.
Premiered at the Sundance Film Festival in January, the film is to have its Canadian premiere at Toronto next month.
On Tuesday, Parker responded to the news of his accuser's death with a Facebook post in which he expressed "profound sorrow".
According to Variety, the 36-year-old will continue to be his film's "public face" and will honour his Toronto media commitments.
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The Toronto Film Festival has said it will screen slavery drama The Birth of a Nation as scheduled, despite ongoing controversy concerning its director.