England's fans had long given up on Thursday's game at Wembley and were entertaining themselves by launching paper aeroplanes towards the pitch by the time Harry Kane stabbed in a predatory 94th-minute winner.
But with two 23-year-olds, 22-year-old Raheem Sterling and 19-year-old Marcus Rashford in his starting XI, Southgate believes it is unrealistic to expect England to play like world-beaters at this stage of their development.
"What the team have been through over 18 months and as a young team what they're having to deal with in terms of expectation and criticism of their performances, it's tough for them," Southgate said.
"They're young players that we have to try and get behind. They're giving absolutely everything they've got. They don't have Champions League or league championship winning medals throughout this group.
"They're a work in progress. But they will give everything they've got for the shirt and they are going to improve over the next few years.
"They're suffering the consequences of 25 years, 30 years, 40 years (of underachievement). That isn't their fault. We have to give them the belief and the backing to go and achieve."
Immediately after the game, the Football Association announced England will play friendlies against Brazil and world champions Germany at Wembley in November.
Their next task is a trip to Lithuania for their final Group F game on Sunday and although it is now a dead rubber, Southgate said he will not release any players from his squad.
"We have to assess where we are injury-wise, but I won't be releasing players," he told his post-match press conference.
"We're a squad. We stay together as a squad. Maybe at some point tonight we might enjoy the fact we're at the World Cup, although that might take a few minutes.
"But there will be England supporters going to Lithuania and we have a duty to put in a performance. We want to stay unbeaten and win the game.
"There are one or two players we're definitely going to have a look at and it's one of few games we have now to build towards the World Cup."
An attendance of only 61,598 -- just over two thirds of Wembley's capacity -- reflected the depths to which England have sunk in the popularity stakes, a year on from their Euro 2016 humiliation by Iceland.
But Southgate said he took solace from the example of the late Bobby Robson, who went from national pariah to national treasure by leading England to the semi-finals at the 1990 World Cup in Italy.
"It's the nature of playing for England and managing England," said Southgate, who stepped into the breach after Sam Allardyce was brought down by a newspaper sting following just one game at the helm.
"We're a country that has high expectations. I've seen Bobby Robson get to a World Cup semi-final and he was hammered up until the quarter-final stage.
"I'm able to rationalise it all. All I have to do is keep winning football matches."
Slovenia coach Srecko Katanec revealed he will step down after his side's final game at home to Scotland.
Slovenia can still mathematically secure a play-off place, but must beat Scotland and hope Slovakia slip up at home to minnows Malta.
"For Slovenian football that means no World Cup," Katanec said.
"But we're working to change the generation and we've brought some young players through.
"Our players were not playing continuously all the time, but I think there's a bright future in front of us."
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