The highly eventful 3-2 win puts Bayern four points clear at the top of the Bundesliga but Dortmund left the match feeling very aggrieved.
The winning goal, scored by Robert Lewandowski, came from the penalty spot after Mats Hummels was adjudged to have handled the ball inside his own box.
However, Bellingham believes the penalty shouldn't have been given and accused referee Felix Zwayer of match fixing in the past.
Bellingham was referring to Zwayer's involvement in a match-fixing scandal in 2005 where Bundesliga 2 referee Robert Hoyzer accepted bribes to fix several matches.
Zwayer assisted him in a Wuppertaler SV match where he had also accepted a bribe. He and three other officials informed the DFB (German Football Association) about Hoyzer's match-fixing, and he was subsequently handed a six-month suspension from refereeing for his part in the scandal.
"For me, it wasn't a penalty," Bellingham said. "He's not even looking at the ball, he's fighting to get it and it hits him.
"You can look at a lot of other decisions in the game. If you give a referee, who has, you know match fixed before, the biggest game in Germany what do you expect?"
Dortmund had their own shout for a penalty turned down with Marco Rose later being sent off by Zwayer for dissent. The Dortmund boss' feelings towards the referee hadn't calmed down after the match finished.
"We all saw what happened," Rose said. "The challenge on Marco Reus is a clear penalty. Mats Hummels' handball is at least arguable, it's a pity.
"Mr Zwayer is welcome to officiate a few more BVB games. He can put a few more obstacles in our way."
Meanwhile, Erling Haaland was also similarly furious with labelling Zwayer's performance as a 'scandal'.
On the Reus penalty claim, Haaland added: "Clear penalty. I asked him [Zwayer] why didn't you go and look [at VAR] and he said 'no need' like arrogant. I have to calm down a little bit now but yeah he was arrogant, I won't say more.'
Haaland later said: "As I said he was very arrogant. It seems like he wanted the headlines and he will get them now because he made many mistakes. He was not a good referee. What can I say? Not a good game from him.
"I totally understand Marco, I support him 100 per cent. I would do exactly the same if I were him.
"It's s***."