Despite Rooney's lack of playing time, Southgate suggested the 31-year-old will be part of England's squad for the World Cup qualifier against Scotland on Nov. 11 and the friendly against Spain four days later.
"He's the England captain and although he didn't start in Slovenia, to me he is a hugely influential person in that group and that won't change," Southgate told British media.
"Let's see what that scenario is but I thought his leadership qualities in the 10 days with us shone through.
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"I haven't spoken to him since the camp but I'm always conscious players are back into a run of fixtures with their clubs, but I will pick up with him and the others later."
Marcus Rashford has been called up for both England's under-21s and the senior side in the past and is backed to replace United team mate Rooney in England's senior team.
Mourinho, however, rejected the idea of him playing for the under-21 side saying it would make "no sense" if the 18-year-old has already established himself in the senior side.
Southgate admitted the youngster should be viewed as somewhere in "between".
"There is a point where young players are still viewed as being part of the development teams," he said.
"There's also a point where we have to decide if they are still in development teams and is that going to benefit them or have they moved through it? As we have seen in the last couple of months Marcus is between the two.
"We have to wait and see what it looks like as we move forward. Everything I have seen Jose say is perfectly reasonable."
(Reporting by Shravanth Vijayakumar in Bengaluru; editing by Sudipto Ganguly)
