The first of two pre-European Championship friendlies at the Riverside Stadium, with around 7,000 fans in attendance, saw the hosts triumph thanks to a goal on 56 minutes from Bukayo Saka, who netted for the first time at senior level for his country.
The Arsenal player was one of five BAME players who started for England, with the others being Jude Bellingham, who impressed on his first senior start, Trent Alexander-Arnold, Tyrone Mings and Jesse Lingard.
Yorkshire-born trio Kalvin Phillips, from Leeds, York-born Ben Godfrey - who made his debut - and Sheffielder Dominic Calvert-Lewin were on the bench alongside Oliver Watkins and Jadon Sancho.
The jeers from some supporters at players 'taking the knee' was drowned out by applause at the anti-racism gesture from the vast majority of the crowd, but the boos did represent an unfortunate down side to a positive night in terms of atmosphere as England played a game in front of fans for the first time in 563 days.
Southgate said: "I did hear it. It’s not something on behalf of our black players that I wanted to hear because it feels like it is a criticism of them.
“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 that the players are doing it. We’re supporting each other.
“I was pleased that it was drowned out by the majority of the crowd but we can’t deny the fact that it happened.
“I think the most important thing for our players to know is that all of their team-mates and the staff are fully supportive."
“I think the majority of people understand it but some people aren’t quite understanding the message and we’re seeing that across many grounds at the moment.”