Berlin's Hertha BSC is contesting its Tuesday loss to Fortuna Düsseldorf that was marred by fan disturbance – and sealed the team's relegation from the first division.
The crowd trouble also prompted Germany's interior minister to tell professional clubs they must agree on clear rules for fans to clamp down on bad behaviour.
Bayern Munich are bidding to lift the trophy for the first time since 2001, having reached two of the last three finals.
Captain Philipp Lahm said his side must beat Chelsea if they want to be considered part of the club's "golden generation". He played in the Bayern team that lost 2-0 at the hands of Jose Mourinho's Inter Milan in the 2010 final in Madrid.
Current club president Uli Hoeneß and chairman Karl-Heinz Rummenigge, meanwhile, were part of the Bayern team that won consecutive titles in 1974, 1975 and 1976.
The Berliners are fighting on a different level. The club's managers said that the chaos ruined the match, and filed a protest that the game did not end fairly, the Berliner Zeitung reported on Thursday.
Düsseldorf fans stormed the field with more than a minute left to play, forcing the referee to stop the game for some 20 minutes. Hertha's lawyer said the team only returned to the field because the police asked them to, fearing an early end to the game would provoke more chaos and even bloodshed.
The German Football Association (DFB) will take up the Hertha protest, filed on Wednesday, at a meeting on Friday, a spokesman said. An investigation has already been launched, while Interior Minister Hans-Peter Friedrich said clubs must get control of their fans.
“All 54 professional football clubs must agree on rules of conduct before the start of the new season,” he wrote in the Kölnische Stadt-Anzeiger newspaper..
Security is expected to be exceptionally tight at Bayern's sold out Saturday game against Chelsea, which netted more than a million requests for tickets.
The Olympic Stadium will be open for public viewing as Lahm will lead the Munich team, eager to make history by lifting the Champions League trophy for the second time and claiming the club's fifth overall European Cup title.
“You need an international title if you want to become a golden generation,” said the 28-year-old.
“You want to lift the cup when you are in a final. And of course it is nice to be the first one to lift it. I don't have many more years at the top level.”
Bayern have been licking their wounds since being hammered 5-2 by Borussia Dortmund in last Saturday's German Cup final and Hoeneß has warned that FA Cup winners Chelsea are a dangerous side.
“Chelsea are a team with their backs against the wall, because of their up-and-down season in the league,” he said.
“If they lose the final, they will not be in the Champions League next season and we all know what that means for a team like Chelsea.
“Anyone who thinks we have already won this match is certainly wrong.”
Bayern are bidding to become the first team since Inter at San Siro in 1965 to win the European title on home soil. Two years after defeat in Madrid, Lahm says the team has grown.
“We have many players who were playing for us in 2010,” said Lahm. “We have developed, we have much more experience. The belief in winning the title is much bigger than two years ago.”