Rooney, making his 117th appearance for his country, was jeered by a small section of the crowd as England toiled to three points in Group F.
The Manchester United and England captain struggled to impress in a midfield role against a Malta team ranked 176th in the Fifa rankings.
But with Rooney subjected to boos from some within the 82,000-crowd, Southgate admitted he was bemused by the treatment of England’s all-time leading goalscorer.
“If you look at the number of games and his (Rooney) goalscoring feats for England, I don’t quite understand that (booing,)” Southgate said. “The criticism of him is, at times, unfair.
“He ploughs on and plays with pride and captains his country with pride. I always look back to the Terrys, the Lampards, the Ashley Coles… in their time with England they took an enormous amount of criticism, but, if you look at their caps, they kept turning out putting themselves on the line.
“Others have not put themselves forward and withdrawn from squads when the going has got tough.
“Those guys put their neck on the block and played for their country again and again.
England vs Malta player ratings
Joe Hart – 6 out 10
Had next to nothing to do. Delivered when called upon late in the game.
Kyle Walker – 7
Up to his usual tricks bombing down the right flank, delivering multiple balls into the box. Untested on the back foot.
John Stones – 6
Composed on the ball and enjoyed a surging run or two down the centre of the park. Faced no real challenges with Malta’s front line.
Gary Cahill – 6
Like his partner, never really put out of his comfort zone. Showed some good cover play.
Ryan Bertrand – N/A
Exited early through injury.
Wayne Rooney – 5
Mediocre performance. Distributed well to the flanks with inch-perfect precision but rarely pressed forward when he needed to.
Jordan Henderson – 7
Created chances with his probing balls into the box and ventured into Matla’s final third to link up neatly with his teammates.
Dele Alli – 6
Missed a series of chances throughout but made up for it with his goal.
Jesse Lingard – 5
Struggled to deliver on the occasion. Missed too many chances. Marcus Rashford would have given England more.
Theo Walcott – 5
Quiet throughout. Didn’t see much of the ball and missed his only opportunity in front of goal.
Daniel Sturridge – 6
Took his goal well to get England off the mark. A busy presence at times around the opposition box but occasionally went missing.
“So I don’t understand (the booing). But that seems to be the landscape. I have no idea how that is expected to help him, for sure.
“I presented him with a cap in the week for being the record cap holder with his country. It’s fascinating to get an insight into his world over the last 10 days. Every debate focuses on him. The onus on him is enormous.”
Rooney’s selection in a defensive midfield role, at the expense of Tottenham’s Eric Dier, was in contrast to Jose Mourinho’s insistence at United that the 30-year-old contributes more as a forward.
But Southgate claimed he had no interest in Mourinho’s view of the player’s best position.
“Look, Jose will have his opinion on what’s right for his team,” Southgate said. “I have to pick a team to get a result today. I don’t see any point in getting drawn into that.
“We knew we’d have a lot of the ball. It was a game where we’d dictate the tempo and his (Rooney) experience, his leadership have been crucial throughout this week, not just today.
“I wanted to get Dele (Alli) higher up the pitch as a link between midfield and the forwards. He got his goal and was disappointed not to get a second, for sure. That team and system suited us today.”
Despite claiming the victory which maintains England’s 100 per cent start to Group F, the performance against Malta failed to hint at progress being made since Euro 2016.
And Southgate, who has called up Arsenal defender Kieran Gibbs to replace hamstring injury victim Ryan Bertrand, admitted his team ‘drifted’ in the second-half.
“I agree (the performance drifted,)” he said. “We, at times, played some really nice stuff in both halves, and had plenty of chances to have made it more comfortable.
“In the second half, subconsciously, there was a feeling the game was won and we were looking towards Tuesday physically.
“We didn’t bomb forward as we might have done had the scoreline been tighter. There’s room for improvement, but that’s not a bad place for us to be.”
England face Slovenia in Ljubljana on Tuesday before returning to Wembley to tackle Scotland on November 11.