Germany players covered their mouths during the team photograph before their World Cup opener against Japan “to convey the message that Fifa is silencing” teams, says Hansi Flick.
The gesture follows Fifa threatening players with a booking for wearing the OneLove armband during games in Qatar.
The captains of seven European nations were set to wear it to promote diversity and inclusion.
No disciplinary action will be taken against Germany.
“It was a sign, a message that we wanted to send out. We wanted to convey the message that Fifa is silencing us,” said head coach Flick after his side’s 2-1 defeat.
Germany and Chelsea forward Kai Havertz said making the gesture was “the right thing to do”.
“Of course, it’s important for us to make a statement like this,” he said. “I think we spoke about the game, what we can do.
“I think it was the right thing to do, to show the people that we tried to help wherever we can and Fifa makes it not easy for us.”
The Germany football federation (DFB) said on Twitter: “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.”
Germany had planned to wear the OneLove armband, along with England, Wales, Belgium, Denmark, the Netherlands and Switzerland.
World governing body Fifa has brought forward its own ‘No Discrimination’ campaign, which had been due to start from the quarter-finals.
Captains will now be permitted to wear a No Discrimination armband for the duration of the tournament.
Germany captain Manuel Neuer wore the Fifa armband against Japan.
“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,” added the DFB.
“Together with other nations, we wanted our voice to be heard.”