He tweeted: “The booing at England game was sickening. Parts of media should stop making excuses for it. It was racism & should be called out.
“If supporting BLM is part of the culture war, then bring it on because you have to stand up against this new wave of racism.”
In a separate tweet sent just minutes later, he added: “In 80s there were those who argued in Labour Party that we should keep our heads down on issues like racism, sexism & LGBT rights for fear of being called loony left & alienating some Labour support.
“Now it’s for fear of being called woke in a culture war. Time to make a stand.”
The comments from Mr McDonnell triggered a furious response from several people on the social media platform.
One wrote: “England fans booed players for taking the knee in opposition to racism/in support BLM.
“Terrible & shaming – highlighting their support of unequal human relations, one-sided dominating exploitation copying stance of govt with its imperial delusions. Wake up UK football supporters.”
One replied: “Have you asked anyone why they boo taking the knee?
“I thought the same as you, but then I asked and I understood it a bit more.
“I didn’t agree with the response, but I didn’t feel it was as simple as racism, at least to me.”
Another wrote: “Sorry John I disagree.
“The co-opting of the BLM movement by football organisations is a tool for creating further divisions within an already fractured society.
“People see through it and have legitimate grievances at the double standards of championing one injustice over others.”
Following the game on Wednesday evening, England manager Gareth Southgate condemned the fans who had booed the players taking the knee before kick-off.
He said: “It’s not something on behalf of our black players I wanted to hear because it feels as though it’s a criticism of them.
“I think we have got a situation where some people seem to think it’s a political stand that they don’t agree with.
“That’s not the reason the players are doing it. We’re supporting each other. I was pleased that was drowned out by the majority of the crowd.”
He added: “We can’t deny the fact that it happened. I think the most important thing for our players to know is all their teammates and all the staff are very supportive.
“I think the majority of people understand it. I think some people aren’t quite understanding the message.
“I suppose we’re seeing that across a number of football grounds at the moment.”