The result ends Rooney's short MLS career. The 33-year-old said prior to the postseason that the 2019 campaign would be his last in the league.
But the late equalizer failed to galvanize the visitors.
Toronto will now do battle with New York City FC at Citi Field on Wednesday.
Greg Vanney's side hadn't won a playoff game since lifting the MLS Cup in 2017. After missing the postseason in 2018, it hit another rough patch in May, going winless over the next eight matches.
TFC rebounded and finished the campaign in fourth in the East, ahead of D.C. United only on goal difference.