Southgate: England selection 'not a popularity contest'
The former Liverpool captain was booed by sections of the Wembley crowd when he was substituted during Friday's 1-0 friendly win over Australia.
Henderson has been criticised for his move to the Gulf kingdom, where homosexuality is illegal, after being a vocal supporter of gay rights during his 12 years at Anfield.
Southgate slammed the supporters' actions as "defying logic" after the Australia match and said it will have no impact on his team selection for Tuesday's Euro 2024 qualifier at home to Italy.
"I will always pick the players who I think are the best players to represent the team, that gives us the best chance of winning - unless I think there is something that is not appropriate," Southgate told reporters.
"People may disagree with Jordan's stance or decision but I don't think that is a reason not to select him. I don't actually think that it is a reason to boo him.
"We would like the fans behind us, we are a stronger team if the supporters are with us. That's the connection we have had for a long period of time. If I select a popularity contest, the team would look different."
Southgate has also been loyal to centre-back Harry Maguire despite his lack of game time at Manchester United and taunting by opposition supporters.
Maguire scored an own goal in last month's 3-1 friendly win at Scotland after having his every touch sarcastically cheered by the home fans.
"I am going to defend our players and our team because we need that unity and strength," added Southgate.
"The two players (Maguire and Henderson) have performed for us in massive games for us. Those characters are the reason we have had big nights."
England only need a draw on Tuesday to secure qualification for Euro 2024.
However, they may also have revenge in mind after losing the Euro 2020 final to Italy on penalties at Wembley just over two years ago.
"We fell short on that night and they're going back to Wembley," said England defender Kyle Walker.
"Hopefully we can get a bit of payback."
Walker is one of the big names expected to return to Southgate's starting line-up after he named an experimental side against Australia.
Italy's place in Germany next year is far from guaranteed with the top two in Group C qualifying.
The Azzurri are tied on 10 points with Ukraine, who they face in their final qualifier next month.