Fans paid their respects at grounds in Dortmund, Moenchengladbach, Hamburg and Frankfurt.
"With this, we would like to show a sense of solidarity with the victims, but also with the citizens of our capital," Dr Reinhard Rauball, president of the German Football League (DFL), had said earlier in a statement
"The compassion of professional football applies to the survivors, as well as to the numerous injured victims, whom we wish a speedy recovery. We are all shaken by what happened on a peaceful Christmas market on Monday evening."
There will be another minute's silence at a further five grounds across the country on Wednesday, including Hertha Berlin's home match against Darmstadt.
That match will take place at Berlin's Olympic Stadium, seven kilometres from Breitscheidplatz where a lorry ploughed into a busy Christmas market on Monday, killing 12 and injuring at least 48 other people.
Bayern Munich host RB Leipzig in a top of the table clash on Wednesday with a sell-out crowd of 75,000 expected at the Allianz Arena.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ