It is the first time since March that the Den has hosted fans after crowds were banned as a precaution during the COVID-19 pandemic.
Derby forward Colin Kazim-Richards, who is Black, described the booing as an "absolute disgrace" in a tweet after the match where he expressed pride in taking a stand against racism.
"Having to say this is a pain," Kazim-Richards said. "But I'll say it every single damn time this is why I STAND and STAND PROUD and I have to say every single person involved with [Derby] did too."
He added that it "made me proud to wear this shirt with the boys today!!!"
The English Football Association condemned the actions of the fans in a statement.
"The FA supports all players and staff that wish to take a stand against discrimination in a respectful manner, which includes taking of the knee, and strongly condemns the behaviours of any spectators that actively voice their opposition to such activities," the statement said.
Some fans had called for the players not to take a knee before the game but Millwall had released a statement on Friday affirming their commitment to fighting racism.
As fans return to Milwall's ground, booing was heard when players took the knee in support of the Black Lives Matter movement. pic.twitter.com/3dcQrVceiF— ESPN UK (@ESPNUK) December 5, 2020
"As a squad we are fully supportive of the entire football family's efforts in ridding the sport, and society generally, of all forms of discrimination," the statement said.
"The gesture of taking the knee before matches provides an opportunity for us to do exactly that and continues to allow all those playing to publicly showcase their support -- on behalf of the whole squad -- for the fight against discrimination.
"We wish to make clear that taking the knee, for us, is in no way representative of any agreement with political messaging or ideology. It is purely about tackling discrimination, as has been the case throughout.
"We will continue to do this until the start of the New Year when a new and comprehensive anti-discrimination strategy will be announced by the club."
Coronavirus regulations in England mean that only 2,000 local fans are allowed to attend games with no away fans permitted to travel.
Footballers in England have been taking a knee before games since football returned in June following protests in the United States over the death of George Floyd in police custody.