After the Fire had spotted Toronto a 1-0 lead, Pappa collected the equalizer in the 64th minute when defender Logan Emory lost control the ball in the box and the Chicago midfielder fired a shot into an open net.
Berry then supplied the decisive tally in the 84th on a header after Toronto had gone down a man on a red card handed out to Emory.
The Fire (10-7-5) improved to 7-2-2 at home with the win.
Ryan Johnson scored for TFC (5-13-4).
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