In its latest disciplinary report, FIFA said both countries breached its code during their 2026 World Cup qualifying playoff final, which DR Congo won on penalties.
The Nigeria Football Federation was fined one thousand Swiss francs after fans were found guilty of throwing objects onto the pitch.
Meanwhile, the Congolese Football Association received a heavier fine of five thousand Swiss francs after supporters used laser pointers during the match.
FIFA said the sanctions were based on the specific circumstances of each incident and remain subject to appeal.
However, the report did not address a separate protest filed by Nigeria over the alleged use of ineligible players by DR Congo.
The Nigerian federation had accused the Congolese side of fielding players with questionable eligibility, but FIFA is yet to rule on the complaint.
Meanwhile, DR Congo have already named their squad for the next stage of qualification.
They are set to face the winner between Jamaica national football team and New Caledonia national football team, with a place at the 2026 World Cup at stake.
