Ezequiel Lavezzi netted after 73 minutes from point-blank range to give Laurent Blanc's men all three points from a frenetic encounter on Sunday.
PSG took the lead 24 minutes into the game, Zlatan Ibrahimovic splitting the home defence with an excellent through ball to allow Edinson Cavani to get his second goal in as many weeks.
Nantes responded excellently and the Brittany club got their reward seven minutes into the second half, as Alex diverted a Jordan Veretout free-kick into his own net to level things up.
The hosts threatened to take all three points at the Stade de la Beaujoire, with midfielder Alejandro Bedoya going close.
However, it was Lavezzi who had the final say, firing in after Lucas Moura's effort had been cleared off the line following a wonderful move that included Ibrahimovic, Blaise Matuidi and Cavani.
Elsewhere on Sunday, Lille bounced back excellently from defeat against Reims last week, as Rene Girard's men dealt Saint-Etienne their first loss of the campaign by securing a 1-0 home win at the Grand Stade Metropole.
A first-half penalty from Salomon Kalou proved to be enough for the 2010-11 champions. The former Chelsea man - now in his second season with Lille - converted from the penalty spot after he was dragged down by midfielder Jeremy Clement.
Elsewhere, Ajaccio are still without a win after being held to a goalless draw by Nice at the Stade Francois Coty.
Fabrizio Ravanelli's men earned a superb point at PSG last weekend, but they could not build on that result in what proved to be a dour spectacle in Corsica, with both sides settling for a share of the spoils from a contest that contained few goalscoring opportunities.