All Germany players took part in the gesture in front of dozens of photographers on the pitch ahead of kick off, after world soccer body FIFA had threatened seven European teams with sanctions if they wore the armband symbolising diversity and tolerance.
Germany's Interior Minister Nancy Faeser, sitting next to FIFA President Gianni Infantino in the stands, sported the armband as she chatted with the football administrator.
Earlier, she had criticised FIFA, saying the threat of sanctions was a mistake and not acceptable behaviour.
"This is not alright, how federations are being put under pressure," Faeser said during a visit to a German FA event in Doha before the game.
"In today's times it is incomprehensible that FIFA does not want people to openly stand for tolerance and against discrimination. It does not fit in our times and it is not appropriate towards people."
A statement from the German Football Association (DFB) said: "We wanted to use our captain’s armband to take a stand for values that we hold in the Germany national team: diversity and mutual respect. Together with other nations, we wanted our voice to be heard.
"It wasn’t about making a political statement – human rights are non-negotiable. That should be taken for granted, but it still isn’t the case. That’s why this message is so important to us. Denying us the armband is the same as denying us a voice. We stand by our position."
Homosexuality is illegal in Qatar.
Germany would go on to lose the game 2-1 Japan after a stunning second half comeback from the Samurai Blue.
