Booing greeted the players as they took a knee ahead of kick-off before there was applause of other supporters to drown out the boos.
England players have rejected the idea the gesture is a political act and Gareth Southgate has said booing feels like an attack on the black players in the squad.
The FA on Sunday issued a plea for fans to support players taking the knee and also released a video calling for unity from in the stands.
“As the team has reiterated many times, they will collectively take the knee ahead of their fixtures during the tournament,” the FA said.
“They are doing this as a mechanism of peacefully protesting against discrimination, injustice and inequality. This is personally important to the players and the values the team collectively represents.
“We encourage those that oppose this action to reflect on the message you are sending to the players you are supporting. Please respect their wishes and remember that we should all be united in the fight to tackle discrimination. Together. They will do their best for you. Please do your best for them.”