Maguire, who began the match on the bench for England, was brought on at halftime due to an injury to Marc Guehi and faced ironic cheers from the Scottish fans for every pass he completed.
The Manchester United defender inadvertently handed Scotland a lifeline by clumsily prodding a low cross into his own net in the 67th minute.
"There has been ridiculous treatment of him for a long period of time, frankly," Southgate said after the match.
"It's a joke. I’ve never known a player treated the way he is not by the Scottish fans, but by our own commentators, pundits, whatever, they've created something beyond anything I've ever seen."
Maguire was stripped of the captaincy by his club Manchester United in July and has struggled for first-team football at Old Trafford.
Nonetheless, Southgate underlined his importance for England, with the centre-back having featured in all of their Euro 2024 qualifying matches.
"He's been an absolute stalwart for us in the second most successful England team for decades. He's been an absolute key part of that," Southgate said.
