The two sides meet at the Etihad Stadium on Wednesday as holders Bayern travel to England for their Champions League Group D clash.
"Last season, Bayern Munich were the team that played the best football and they became European champions, so if you beat them, people on the outside will notice," Fernandinho told reporters. "It would be a huge statement to the football world if we could beat the best team in Europe, one of the best teams in the world.
"The projection would be much higher than beating United. That is why a win for us would be so important. The United match was all about playing your local rival. It was a derby and you always want to beat your neighbours, so the atmosphere is different for the players, manager, directors, supporters – everybody.
"It is different from a normal game. You don't play against United and picture them as the champions, you just regard them as your local rivals. The game against Bayern Munich is different, they are the best around."
Fernandinho joined City for £30m from Shakhtar Donetsk in the summer.