Neymar, 27, was targeted by fans during the 3-0 victory at Parc des Princes on August 11 amid growing speculation he wants to leave PSG.
One banner urged the Brazil forward to leave the Ligue 1 champions, 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."
The saga is seemingly no closer to ending despite the transfer window closing on September 2.
Neymar has scored 51 goals in 58 games since joining PSG in a world-record €222million move two years ago.