"Remembering the victims of the Hanau attacks," the Bayern Munich club said on Twitter.
A minute of silence was observed at the Allianz Arena in Munich before a match between Bayern Munich and Paderborn.
Bayern Munich's tweet showed players wearing black armbands.
Paderborn posted a photograph displaying players from both teams standing in silence.
"In memory of the victims in Hanau," Paderborn said.
Bundesliga and its lower division, Bundesliga 2, will remember Hanau victims this weekend, German Football League (DFL) said Thursday.
"Bundesliga and Bundesliga 2 will commemorate the victims of Hanau this weekend with a minute's silence. On Matchday 23 the teams will also wear black armbands," DFL said.
DFL Executive Committee spokesperson Christian Seifert said it was in shock hearing of the "murders of Hanau" but German football will offer condolences to relatives of those killed in the shootings.
"The murders of Hanau are an appalling crime. This act leaves us in shock and disbelief. German professional football as a whole will send a message of condolence this weekend. Our thoughts are with the victims and their relatives," Seifert remarked.
Two other Bundesliga clubs, Borussia Dortmund and rivals Schalke 04 each condemned the attack on social media.
"Our thoughts and support are with all those who lost and were affected by the terrible attack in Hanau," Dortmund said on Twitter. "Borussia Dortmund stands against all acts of racism, extremism, and discrimination #BorussiaVerbindet (BorussiaUnites)."
Schalke said: "German football will pay its respects to the victims of the terrible crimes committed in #Hanau this weekend. There will be a minute's silence before #S04RBL (Schalke vs RB Leipzig), and both teams will wear black armbands. Our thoughts are with you."
Four Turkish nationals were among nine people killed in the attack near Frankfurt late Wednesday, according to Turkish officials.
The gunman, identified by security forces as Tobias R., 43, posted racist videos online before the attack, and afterwards was found dead at his apartment.