However, that does not mean the Three Lions boss will consider England's record goalscorer for a future call-up.
"We have a lot of players playing exceptionally well in the area of the pitch that Wayne plays," Southgate said at a news conference.
"I said last time [in March] that he was a bit short of matches, he has had some matches now but we have got players that have done really, really well for us in Adam Lallana and Dele Alli.
"We have got Marcus Rashford, Harry Kane coming back and Jermain Defoe who did really well for us last time while Jamie Vardy has been in excellent form in the second half of the season. I cannot dress it up any other way. Other players are in really good form and deserve to keep their place.
"I have showed that, by selecting Jermain Defoe at 34, if players are playing well and the moment is right then we will involve them in the squad.
"You never write off a player of Wayne's quality and I am sure that, next season, he will be back to playing. He has finished the season a bit better and I am sure he will take that into next year."
While confident that Rooney will see more minutes in 2017-18 than he managed at United this season, Southgate acknowledges that he faces some important decisions - with speculation building regarding an imminent exit from Old Trafford.
"I've no idea what the future is for Wayne at Manchester United so it's impossible for me to comment if he's part of the plans or not," he added.
"He's got some big decisions to make this summer - you want your players playing in the biggest possible games."
Meanwhile, Southgate will be without Nathaniel Clyne for the upcoming games after the Liverpool defender was forced to withdraw from the squad with a back injury.