The fans carried banners with messages such as "Keep our fan culture", "We don't want tennis crowds" and "Football lives through its fans" as they continued to put pressure on clubs and the German Football League (DFL) ahead of a meeting on Dec. 12.
The DFL's proposal includes frisking at high risk games, tougher sanctions for the use of pyrotechnics and seating-only areas for away fans.
Around 1,000 fans of Bavarian rivals Augsburg and Bayern Munich marched together through the streets before their Bundesliga game which Bayern won 2-0 and there were also marches in Dortmund, Paderborn and Dresden.
For the second week running, fans at first and second division matches remained silent for the first 12 minutes and 12 seconds of matches, creating an eerie atmosphere where the shouts of the players could be heard, before bursting into life.
At Borussia Dortmund's match at home to VfL Wolfsburg, fans counted down the final few seconds of silence before throwing toilet rolls onto the air in South American style.
"The protests have been a complete success," Philipp Markhardt, spokesman for the supporters' organsiation Pro Fans, told German media. "Everyone has heard and seen us."
German supporters are intensely proud of their culture, saying the raucous flag-waving atmosphere at their stadiums is a far cry from other countries such as England.
The Bundesliga allows standing areas in its stadiums, the largest being Borussia Dortmund's 25,000 capacity Suedtribune. The terraces are converted to seats for European competition.
The DFL's initiative came as a police report last month said the 2011/12 season had the highest number of criminal proceedings in 12 years, almost double the amount of injured fans and a more than 20 percent rise in police work hours from the previous season.
Widespread crowd trouble before October's Ruhr valley derby between Dortmund and Schalke 04 and more fighting when Hanover 96 met Dynamo Dresden in the German Cup days later have fuelled concern at the problem. (Writing by Brian Homewood in Berne; Editing by Tom Pilcher)