The FA will take no disciplinary action over the crowd-related incidents at Millwall and Colchester on December 5.
The governing body launched an investigation after some supporters booed players taking a knee.
While no further action will taken, the FA says it will continue to support anyone who chooses to take the knee, and added that it does not view the anti-racism gesture as a political symbol.
An FA statement read: "The FA has conducted full and thorough investigations into the crowd-related incidents that took place at both The Den and JobServe Community Stadium on Saturday, December 5 2020.
"Having carefully considered these matters, including the observations from all relevant parties, we can confirm that no formal disciplinary action will be taken against the clubs concerned on this occasion.
"However, The FA would like to further clarify that anyone who chooses to take the knee will continue to receive our support as they highlight the inequality and injustice experienced by the Black community.
"To be clear, we do not see taking the knee as a political symbol, and would contend that there can now be no doubt as to what the gesture means in a footballing context.
"Therefore, going forward, The FA will continue to monitor and investigate should similar crowd-related incidents occur.
"The FA continues to support all players and clubs that wish to take a stand against any form of discrimination, and will always condemn the behaviours of anyone that chooses to actively oppose these values."
Millwall said they were "dismayed and saddened by events which marred their game against Derby County" while Colchester owner Robbie Cowling says fans who want to boo players taking a knee are not welcome at the club.
PFA survey shows players wish to continue taking a knee
A Professional Footballers' Association survey has shown players overwhelmingly support continuing to take a knee.
The PFA sent a questionnaire to all its members asking whether it should continue after a series of incidents where fans booed the anti-racism gesture, and how best the leagues, clubs, and players should express the anti-discrimination message.
The results showed that 80 per cent of players 'support continuing this act of solidarity despite any adverse responses that may be received', with over 400 responses to the survey.
A PFA statement read: "Throughout 2020, PFA members have demonstrated a strong understanding of the societal issues raised across the world and have used their platform to highlight the impact racism has on both individuals and wider communities.
"The decision to take the knee before matches was initially made by Premier League captains during Project Restart, to show solidarity with Black people facing discrimination globally.
"This powerful symbol of solidarity represents the players' commitment to anti-racism and is not an endorsement of any political position. It is a peaceful act of unity that highlights a persistent and systemic issue."