Toronto was playing with 10 men after Doneil Henry was sent off in the 41st minute with his second yellow card, but midfielder Jonathan Osorio still managed to put Toronto ahead in the 66th with a diving header.
Philadelphia, however, responded in the closing moments when McInerney's low shot in the 90th minute went in for the equalizer.
The Union improved to 5-5-4.
Toronto (1-7-5), meanwhile, let a victory slip away en route to extending its winless streak to 12 games.
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