Some Millwall supporters booed when players from both sides took a knee before the Championship match, which Derby won 1-0.
The Den was able to host 2,000 fans with London placed in tier two of the current system of coronavirus restrictions, but the return of spectators was overshadowed by the pre-match incident.
Kick It Out chair Sanjay Bhandari told the PA news agency: "We are saddened by the behaviour of fans booing the players taking the knee today at Millwall.
"What this demonstrates is that players are right to continue standing up to discrimination, whether that is through taking the knee or speaking out.
"The fight for racial equality continues and we will continue to work closely with clubs across the country to tackle discrimination in all its forms.
"We urge the players to continue using their platforms and their voices to support this fight.
"We applaud the players of Millwall and Derby for taking a stand and defying the hate shown by some fans today."
Fans were back at The Den for the first time since February 29, but their long-awaited return was quickly mired in controversy.
In footage seen on social media, booing from the stands is clearly heard after referee Darren England blows his whistle for the players to take a knee, a gesture used to show support for the fight against discrimination following the unlawful killing of George Floyd in America earlier this year.
The Football Association condemned the behaviour of the Millwall fans. A spokesperson said: "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."
Derby forward Colin Kazim-Richards made his feelings about the booing clear after the match.
He tweeted: "Having to say this is a pain 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 dcfcofficial did too made me proud to wear this shirt with the boys today!!! Absolute disgrace.."
But having to say this is a pain 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 @dcfcofficial did too made me proud to wear this shirt with the boys today!!! Absolute disgrace.. pic.twitter.com/lVsdb1KUpa
— Colin Kazim-Richards (@ColinKazim) December 5, 2020
Millwall manager Gary Rowett, who saw Jason Knight grab Derby's winner, expressed his disappointment at the incident, but said his players were concerned that taking the knee was in danger of becoming an empty gesture.
He said: "The players have released a statement together and said they don't support it [taking the knee] as a political message but support anti-discrimination.
"Moving forward, like a lot of clubs, they would prefer not to take the knee and actually enact change.
"They want to be proactive rather than it being a gesture which a lot of clubs are now saying is perhaps empty.
"That's not my consideration, but they now feel that gesture is in danger of being empty."
Ahead of the Championship match, the topic was discussed on Millwall's fans' forum and a statement from the first-team squad was published on the official club website on Friday.
It read: "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.
"It is our duty as players to reinforce the positive messaging and action of clubs, community trusts, charities and governing bodies, and we do so with great pride and knowledge that so much good work is being done up and down the country.
"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."
The EFL later signalled its continued support for clubs and players who wish to take the knee.
We are disappointed that a small group of supporters have today chosen to voice their opposition to such activities directly aimed at raising awareness of the fight against racism. #EFL | #NTOAD pic.twitter.com/6UToYBayAv
— EFL Communications (@EFL_Comms) December 5, 2020
A statement said: "The EFL continues to support any individual player, players and clubs who choose to 'take the knee' in support of tackling inequality in society.
"We are disappointed that a small group of supporters have today chosen to voice their opposition to such activities directly aimed at raising awareness of the fight against racism.
"Discrimination in any form is not welcome and we remain committed to working with our clubs, including Millwall who undertake a significant amount of work on equality and inclusion initiatives, as we continue with our collective objective to eradicate all types of prejudiced behaviour, ensuring the EFL is an inclusive and diverse environment for all."
Additional reporting by PA.