The match will be Rooney's 120th appearance for England and a final opportunity to add to the record 53 goals he has amassed so far.
Southgate revealed that Rooney did not want to distract the squad ahead of the tournament, and also insisted it was the right decision to call up Rooney to face the United States on November 15.
But he said he was relieved to be able to offer Rooney a tribute after dropping the forward from the England squad shortly before the player's retirement from worldwide football.
"But I can understand why some people might think it makes the game a bit of a circus - and England have got an important game (a crucial Nations League decider against Croatia) three days later".
"I am still able to look to the future in terms of the squad we have picked", insisted Southgate. "This game is the first opportunity we've had at Wembley to do that".
"I've not spoken to Gareth (Southgate) too much about how he's going to do it when we play but it'll be great to see him again and I'm sure he's looking forward to seeing a few of the boys".
Injuries and the fitness of other players may determine whether or not Southgate hands a shock call up to 18-year-old Nelson, who has been impressing in the Bundesliga.
"He wouldn't wear the No 10 because he won't start the game", Southgate said.
"Having said that, we've given caps to people who haven't earned them in the past - I'm not going to name names - and you do wonder how on earth they got them".
"So I guess that will depend on the circumstances around the game and the players that are on there but I have no issue with that at all".
Bournemouth striker Callum Wilson and Brighton defender Lewis Dunk have been handed call-ups by Southgate for the friendly against the US and the UEFA Nations League clash with Croatia.
Ruben Loftus-Cheek, Dele Alli and Jesse Lingard have been included in the squad after missing the most recent internationals.