Rooney has held the armband since the summer of 2014 but his dwindling form and questions about his future at Manchester United have seen him fall out of favour and he was a notable omission from the squad for the upcoming games with Germany and Lithuania.
Kane is another absentee due to an ankle injury but despite also missing Southgate's other matches in charge due to fitness problems, is very much seen as a key player for the Three Lions going forward.
He also has captaincy experience having led Tottenham at times in the absence of Hugo Lloris.
Although Liverpool's Jordan Henderson has previously worn the armband, his own injury problems mean Gary Cahill looks the man most likely to skipper the national team over the next fortnight.
Neither appear to be Southgate's first option though, with the coach hinting that Kane would be his preferred option for the future.
"Harry has definite leadership qualities," he said. "He's a very determined, single-minded individual, completely dedicated to improving and he's having another outstanding season.
"He is in his third season now of playing at a very high level and getting high numbers of goals. It's great.
"But it looks good for him. And for Tottenham and England. He's vocal and Harry's got an opinion, yeah. He's always happy to speak up in front of the group. As are several others."