The German players covered their mouths during the team photo before their World Cup opener against Japan amid the dispute with Fifa over the OneLove armband.
The gesture follows Fifa’s threat to the players being booked for wearing the OneLove armband during games in Qatar.
Captains from seven European nations had to wear it to promote diversity and inclusion.
“It was not about making a political statement,” the German Football Federation (DFB) said on Twitter.
“Human rights are non-negotiable. It should be taken for granted, but it still isn’t. That’s why this message is so important to us.
“To deny us the armband is to deny us a vote. We maintain our position.”
Germany were among the teams that had planned to wear the OneLove armband, along with England, Wales, Belgium, Denmark, the Netherlands and Switzerland.
Fifa launched its own “No Discrimination” campaign, which was to start from the quarter-finals.
Captains will now be allowed to wear an anti-discrimination armband for the duration of the tournament.
German captain Manuel Neuer wore the FIFA armband against Japan.
“We wanted to use our captain’s armband to defend the values that we carry in the German team: diversity and mutual respect,” added the DFB.
“Together 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.
“They combined that with massive threats of sporting sanctions without specifying them.
“The DFB is checking whether this action by Fifa was legal.”
Simon told German outlet Bild that the DFB has contacted the Court of Arbitration for Sport (Cas) over the matter and hopes Neuer can wear the OneLove armband for his side’s second Group E game against Spain on Sunday.
Danish Football Federation chief executive Jakob Jensen said the seven nations that had planned to wear the OneLove armband are “coordinating” discussions about their next legal steps.
However, he said it was “not possible” to go to Cas about it.
He added: “If you want to go through Cas, you first have to complain within the Fifa system, you have to go to the appeal body, and then you can go through Cas.”
Simon said earlier that the seven nations were in the face of “extreme blackmail” from Fifa.
German supermarket chain Rewe has suspended its advertising deal with the DFB in a bid to distance itself from Fifa.
Harry Kane wore the Fifa armband as England kicked off their World Cup campaign with a 6-2 win over Iran on Monday, with the Three Lions players also taking the knee before kick-off.
It was announced in September that the captains of 10 European nations – England, Wales, Belgium, Denmark, France, Germany, Norway, Sweden, Switzerland and the Netherlands – would wear a OneLove armband during Nations League matches and the World Cup.
Norway and Sweden failed to qualify for the World Cup while France captain Hugo Lloris said he would not wear the armband as he wanted to “show respect” to Qatar.
The Netherlands launched the OneLove campaign ahead of Euro 2020 to promote diversity and inclusion, and as a message against discrimination.
Same-sex relationships and the promotion of same-sex relationships are criminalized in Qatar, as they are considered immoral under Islamic Sharia.
Meanwhile, former England winger Andros Townsend said he was “a bit uncomfortable” over protests over Qatar’s stance on LGBTQ+ rights in the country given its basis in Sharia law. Islamic.
Speaking on TalkSport, the Everton striker said Muslim players respect campaigns such as the rainbow laces in the UK, but “cannot promote them as they fear go against their religion.
He added: “It’s difficult – when they are in our country, they respect our beliefs. We come to their country, we don’t agree, but it’s still their religious belief.
“I’m a little uncomfortable that we’re coming here to protest and disrupt a culture while these guys are in their own country.”
