Germany players covered their mouths in the team photo before the World Cup match against Japan for the OneLove armband with FIFA.
The gesture threatens FIFA players with a ban on wearing the OneLove armband during matches in Qatar.
Captains from seven European nations dressed up to promote diversity and inclusion.
“It was not a political statement,” the German Football Association (DFB) said on Twitter.
“Human rights are non-negotiable. That should be taken for granted, but it still isn’t. That is why this message is so important to us.
“Denying an arm is the same as denying us a voice. We stand by our position.”
Germany was one of the teams scheduled to wear the OneLove armband, along with England, Wales, Belgium, Denmark, the Netherlands and Switzerland.
FIFA has launched its “No Discrimination” campaign, which was supposed to start from the quarter-finals.
Captains will now be allowed to wear a Non-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 support our values in the German national team: diversity and mutual respect,” the DFB added.
“Along with other nations, we wanted our voice to be heard.”
The DFB says it is investigating whether FIFA’s threat to punish players for wearing the armband is legal.
“FIFA has banned us from using a symbol of diversity and human rights,” said DFB media director Steffen Simon.
“That was combined with unspecified mass threats of sports sanctions.
“The DFB is checking whether this action by FIFA was legal.”
Simon told German media outlet Bild that the DFB has contacted the Court of Arbitration for Sport (Cas) over the matter and hopes Neuer will be able to wear the OneLove armband for Sunday’s Group E second leg against Spain.
Danish Football Federation CEO Jakob Jensen said the seven nations that had planned to wear the OneLove armband are “coordinating” discussions about their legal next steps.
However, he said “it is not possible” to go to Cas on the issue.
He added: “If you want to go through Cas you have to complain within the Fifa system first, you have to go to the appeals body, then you can go through Cas.”
Simon has previously said the Seven Nations were facing “extreme blackmail” from FIFA.
German supermarket chain Rewe has canceled its advertising deal with the DFB in a bid to distance itself from FIFA.