Rooney was booed by some members of the Wembley crowd during Saturday’s 2-0 victory over Malta, in which he played in a deep-lying midfield role.
Southgate said afterwards that he “didn’t understand” the reaction of those supporters and insisted he was happy with the 30-year-old’s performance.
But with Eric Dier pushing for a starting spot in Tuesday’s World Cup qualifier in Ljubljana, Southgate has made it clear that he will not pick players on reputation.
“I’ve got to make decisions which are right for the team and whenever you select a team, with England, you’re going to leave some guys on the bench that are playing every week in the Premier League for their club,” he said.
“You have to be prepared to do that. That’s part and parcel of the job.”
Rooney has not started a game for Manchester United since the 3-1 Premier League defeat to Watford on September 18, but Southgate insists that his selection will not be based on club performances.
“I think at this moment in time, that [lack of football at United] is irrelevant,” he said. “Part of that is because we’ve got 30 per cent of the Premier League eligible for England.
“Of that, some don’t want to play, some aren’t good enough to play and you’ve got a captain who is desperate to lead on and off the field and continues to make an outstanding contribution to that group of players.
“So that was why he was selected. What’s happening at Manchester United for this week is not as important.
“I was very pleased with Wayne’s performance. I felt the role he was asked to play he fulfilled. He was asked to dictate the game, play with positional discipline which we thought was very important. Him and Jordan Henderson as a pair did exactly as we hoped.
“Slovenia is a completely different game, we are likely to be playing against a different tactical system and away from home, so we have to assess all those things with all the players to pick the right team for that game.
“Wayne commands respect. When he makes his observations, he speaks up, it’s clear the authority that he talks with, but also the insight and his knowledge of the game is of a very high level, not just of the game but the dynamics of the groups and things they can learn, things they can improve upon. But it’s impossible to really feel that unless you are inside it.”