Bellingham made reference to Zwayer’s six-month ban for his involvement in a match-fixing scandal back in 2005 after Dortmund lost 3-2 to Bayern Munich in controversial circumstances at the Signal Iduna Park.
The victory moved Bayern Munich four points clear of Dortmund at the top of the Bundesliga standings.
Zwayer awarded Bayern a penalty for a Matts Hummels handball after waving away Dortmund’s appeal for a spot kick earlier in the game for a challenge on Marco Reus.
Interviewed after the game by Viaplay, Bellingham said: "For me, it wasn't [a penalty]. He [Hummels] is not even looking at the ball and he's fighting to get it and it hits him. You can look at a lot of the decisions in the game.
"You give a referee that has match fixed before the biggest game in Germany. What do you expect?"
The DFB released a statement on its website on Tuesday saying: "The Sports Court of the German Football Association (DFB) has fined Jude Bellingham in the amount of 40,000 euros in single-judge proceedings after indictment by the DFB Control Committee for unsportsmanlike conduct.
"The player of the Bundesliga club Borussia Dortmund has already agreed to the verdict, the verdict is therefore legally binding."
18-year-old England international Bellingham has made 21 appearances in all competitions for Dortmund this season, scoring three goals and providing seven assists.
