Neymar, 27, was targeted by fans during the 3-0 victory at Parc des Princes on 12 August amid growing speculation he wants to leave PSG.
One banner urged the Brazil forward to leave the Ligue 1 champion, while another expressed dissatisfaction with his behaviour.
The Ligue de Football Professionnel (LFP) Disciplinary Committee announced sanctions on Wednesday, handing PSG a fine.
"Behaviour of the supporters of Paris Saint-Germain: use of pyrotechnic devices and deployment of an offensive banner," part of a statement read.
"€2,000 fine for Paris Saint-Germain."
Neymar is yet to play for PSG this season amid reports he will return to Barcelona or join LaLiga giants Real Madrid.
The saga is seemingly no closer to ending despite the transfer window closing on 3 September (AEST).
Neymar has scored 51 goals in 58 games since joining PSG in a world-record €222million move two years ago.