Brown had been the odds on favourite to lead Scotland at the last Six Nations but the broken ankle he suffered in Saracens' Heineken Cup win over Treviso in January ruled him out of contention.
Ross Ford led the Scots in his absence but Brown will take over for the November Tests with New Zealand, South Africa and Tonga despite the fact that the Lions hooker guided his side to three wins from three games on their summer tour of the southern hemisphere.
"Kelly Brown is an inspirational person. He has an aura, confidence and belief about him and a firm understanding of the game," said Scotland head coach Andy Robinson.
"He has been a very consistent performer for Scotland. It's because of these qualities that he has been appointed Scotland captain."
But while 30-year-old Brown will lead his country out on the day of his 50th cap a week on Sunday, it remains unclear whether 2009 Lions captain Paul O'Connell will do the same for Ireland against South Africa.
O'Connell hopes to win his 86th cap for Ireland in the Aviva Stadium encounter with the side who beat his pride of Lions three years ago but a back problem could prevent him from doing so.
And with regular Ireland captain Brian O'Driscoll and stand-in skipper Rory Best both ruled out of the November games with injury, Kidney has decided to delay announcing who will wear the armband against the Boks.
"We'll assess all that now. Paul (O'Connell) isn't training today, he has his own niggles with his back. He was hoping to get a bit of pitch-time this weekend," said Kidney.
"Captain can be an onerous position. We'll let him recover first. We'll look after the person first and then see what's right for the team."