The 31-year-old regained his place in the Three Lions’ starting line-up last Friday, when he helped secure a 3-0 win against oldest foes Scotland in a crucial World Cup qualifier at Wembley.
A minor knee injury saw Rooney withdraw from the squad on the eve of Tuesday’s 2-2 draw with Spain, with Southgate forced to deny the absence was anything to do with images that emerged from The Grove hotel on Saturday night.
Pictures showed Rooney sporting an England training top, looking the worse for wear.
The FA is to review players’ free time as a result of an incident that led Rooney to apologise in private to interim boss Southgate and the governing body’s technical director Dan Ashworth.
In a statement issued on Rooney’s behalf, the player’s spokesperson said: “Naturally Wayne is sorry that pictures taken with fans have been published today.
“Although it was a day off for the whole squad and staff, he fully recognises that the images are inappropriate for someone in his position.
“Earlier today Wayne spoke privately to both Gareth Southgate and Dan Ashworth to unreservedly apologise.
“He would like to further extend that apology to any young fans who have seen these pictures.”
What Manchester United manager Jose Mourinho thinks about the matter will become clear when he addresses the media tomorrow ahead of the Premier League clash with Arsenal.
Rooney has endured a tough campaign, finding himself in the unusual situation of fighting for his place in the team.
The 31-year-old ended his goal drought in the recent Europa League clash at Fenerbahce and impressed as United headed into the international break with a 3-1 win at Swansea.
Rooney dropped to the bench in last month’s qualifier in Slovenia, but returned to the starting line-up as Scotland were beaten at Wembley.
United return to action on Saturday lunchtime against Arsenal, before hosting Feyenoord in the Europa League. England are not in action again until March’s glamour friendly in Germany.
Meanwhile Tottenham midfielder Eric Dier has hailed Gareth Southgate’s impact after praising the brand of football imposed during his caretaker four-game stint.
Whether or not Southgate continues in the post on a permanent basis now lies with the FA but the 46-year-old’s emphasis on methodical attacking and building play from the back has gone down well in the dressing room.
England were held 2-2 by Spain at Wembley on Tuesday night, with goals from Adam Lallana and Jamie Vardy cancelled out in the closing seconds, Spain finishing with a flourish as Iago Aspas and Isco grabbed a dramatic late draw.
While the result was disappointing, for Dier, who learned his trade in Portugal’s more technical system and grew in stature under Mauricio Pochettino’s progressive regime at Spurs, the passing game England displayed under Southgate at Wembley remains the only way to proceed.
“I don’t care what the result is, I want us to have a style of play and a way of playing that we stick to,” he said.
“Win, lose, or draw I’ll be happy as long as we stick to a way of playing and believe in it 100%. Gareth is the same way, I don’t think anything should change for him. It’s important people don’t change and stick to their beliefs. I think that’s what we’ve been doing over these four games now and you could see it [against Spain] better than in the other three.
“We had a way, we stuck to it and we got our rewards up until the end. I think at times you can be half-hearted — you play out and then you lose the ball playing out so you want to go long; you go long and it’s ‘why didn’t you play out?’.
“You either do it or you don’t, for me, with or without the ball. I think we’ve been getting better at that.”
Southgate is taking a few days off to reflect and review as the FA decides whether to give him the England job on a permanent basis.