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Neymar opened the scoring early in the second half to give Christophe Galtier's home side the lead, but substitute Marco Verratti was sent off soon afterwards.
PSG continued to have the better chances but could not extend their lead, though the 10 men still looked set to grind out a valuable win to return to winning ways on Ligue 1 duty.
Balogun had other ideas though, latching onto Kamory Doumbia's throughball to slot past Gianluigi Donnarumma in the sixth minute of stoppage time and stun the home crowd.