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Maguire is experiencing one of the most difficult periods of his career after being dropped by Manchester United boss Erik ten Hag following criticism of his performances over the last 12 months.
Ten Hag has largely preferred to play new signing Lisandro Martinez alongside Raphael Varane at centre-back this season, with Maguire forced into a bit-part role.
His decision to bench Maguire has created a major problem for Southgate just months out from the World Cup in Qatar, with his first-choice centre-back now struggling for minutes.
Maguire is, however, expected to start for England in Friday's Nations League match against Italy at San Siro.
Southgate has given his full support to Maguire and is hopeful the defender can fight his way back into United's starting XI before the World Cup.
"Clearly, it's not an ideal situation [with Maguire]," said Southgate.
"We're only a few weeks on from pre-season so, physically, if they've had a few 90 minutes, that's fine. Another seven to eight weeks, that does start to become more complicated.
"But he is an important player for us and it's important to back our best players. Whatever reputation I have, I'm putting it on there. He is our most dominant aerial centre-back.
"Him and John [Stones] are incredible with the ball – the amount of pressure they have taken for the team in tournaments because we don’t always have that midfield pivot player who can progress the game.
"It means there is a huge amount more pressure on our centre-backs to use the ball well and those two are as good as any in world football at doing that."
Southgate is expected to revert to a back three against Italy, as he looks to get his side back to winning ways after a disappointing June international break.
England were held to draws by Italy and Germany, before losing 4-0 at home to Hungary - a defeat that has left them bottom of their Nations League group with just two points from four games.
"We were 22 games without a loss [apart from the Euro 2020 final penalty shootout defeat against Italy] and for everybody you think that's just going to continue and maybe you are not quite as ruthless on certain decision making," Southgate said, explaining England's dip in form over the summer.
"I compromised in one or two things. When you have a difficult run it hardens your resolve. We are very clear on why those things happened and what needs to happen to put those things right.
"Every manager makes mistakes. Every manager reflects. I am not saying I was comfortable. I was saying generally at times, when you are on a big run, you don't dig as deep into what could be ahead and what could go wrong.
"The summer was really complicated but we reviewed everything and there were things we should have done better. Quite often when you win some of those things are still going on but you don't review it with the same intensity."