One banner urged the Brazil forward to leave the Ligue 1 champions, while another expressed dissatisfaction with his behaviour.
Chants of "Son of a bitch" also rang out in the stands among home fans incensed at the failure of the player to commit his future to the club this summer..
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 €222 million move two years ago.
But he is yet to appear in the 2019-20 campaign after suffering an injury during Brazil's preparations for the Copa America in June, as PSG kicked off their Ligue 1 defence with mixed fortunes.
That 3-0 defeat of Nimes was followed by a humbling reverse at the hands of Rennes, who upset the champions 2-1 on Sunday.