Cambridge manager Mark Bonner said fans who booed the taking of the knee before his side’s win over Colchester were “embarrassing” and “unacceptable”.
Applause drowned out the initial jeering as the gesture was made before the League Two match.
“We don’t stand for that at all here,” said Bonner of the boos.
“It’s an anti-discrimination message talking about racism, systemic racism and inequality. We’ve backed that with Colchester and everyone should.”
It was the first time the gesture has been made at the Abbey Stadium since fans were allowed back at the venue.
Cambridge United went on to win the game 2-1.
“A small minority of fans booed and that is embarrassing and unacceptable,” added Bonner.
“The best thing we can do is stand up and give credit to the vast majority of people who behaved in the right way, in a way that represents our club properly.”
Cambridge player Harvey Knibbs said he was “appalled and embarrassed” by the fans who booed.
“It’s 2020 and the action is a symbol of solidarity,” he said on social media.
“I want to thank the fans who overhauled the boos with applause but this cannot continue.”
League Two side Exeter City said one supporter was ejected from the stadium after players took the knee before their game against Harrogate Town.
Exeter thanked “the vast majority” of fans for supporting players taking the knee but said they would take “the appropriate action” against the spectator who was removed.
Earlier this month some Colchester fans booed players taking the knee before their game with Grimsby.
Club owner Robbie Cowling was heavily critical of those who booed before the 5 December fixture, saying that any repeat offenders would no longer be “welcome at our club”.
On the same day as the incident at Colchester, Millwall fans also jeered players for taking the knee before a defeat by Derby. The Millwall team had released a statement earlier in the week explaining that their gesture carried no political message, but was “purely about tackling discrimination”.
The gesture first came to prominence when San Francisco 49ers quarter-back Colin Kaepernick chose to kneel rather than stand for the US national anthem before a game in September 2016 as a protest against police brutality.
After the death of George Floyd, a 46-year-old man who died after a Minneapolis policeman knelt on his neck for several minutes, it became widespread in global protests against racial injustice and violence.