The three points lifted Dijon into third from bottom in the Ligue 1 table while PSG will now need to regroup before facing Club Brugge in the Champions League.
Barcelona attempted to re-sign Neymar, sold to PSG for a world record 222 million euros ($249 million) in 2017, but the two teams were unable to agree a deal.
Ballon D'Or, the holder of the men's award, Luka Modric, and the world's most expensive player Neymar missed out as France Football unveiled nominees in four categories.
In an attempt to win over PSG fans, Neymar has looked a rejuvenated figure, scoring for a third time this season.
The Neymar-Barcelona dispute focuses on the contract renewal bonus that was signed between the player and the club in 2016.
Lyon vs Paris Saint-Germain: PSG followed up their impressive midweek Champions League victory over Real Madrid with the win in constant drizzling rain in Lyon.
The Court of Arbitration for Sport reduced Neymar's three-match Champions League ban to two games following an appeal.
Neymar was booed and insulted by sections of the PSG support in the Ligue 1 match against Strasbourg at the Parc des Princes.
Lionel Messi denied reports he had used his influence to try and force the Barcelona board to push through the deal.
Sao Paulo prosecutors said in a statement that investigators had found "indications of slanderous denunciation and extortion" in the woman's accusation.
Neymar has not featured at all for his current club this season amid the uncertainty surrounding his future.
The deal which the Barcelona officials will propose could include other players such as Philippe Coutinho or Ivan Rakitic.
Home fans unfurled a banner before kick-off translating to "Neymar. Get out".
Rumours surrounding Neymar's transfer continue to swirl unabated as the new Ligue 1 season kicks off this weekend.
Kylian Mbappe also doused any lingering concerns over his own plans after he talked about playing "elsewhere" at the French league awards ceremony in May.
The police decision will be sent to prosecutors on Tuesday, who will have 15 days to evaluate the case.
When Neymar missed last Monday's first training session, PSG had issued a statement declaring they would take "appropriate action" against the star.
PSG were upset at Neymar's no-show at the resumption of training last week, an absence that fuelled speculation of his possible departure back to Barcelona.