South Africa open their Rugby Championship campaign against Argentina on August 19 at Nelson Mandela Bay Stadium in the eastern coastal city.
Lock Etzebeth debuted as skipper in a 35-12 victory over France two months ago that wrapped up a season-opening 3-0 series success after a disastrous eight-loss 2016 campaign.
“Eben did an excellent job against France in Johannesburg when he had to step in at short notice after the late withdrawal of Warren,” Coetzee told reporters.
“He enjoys the respect of his team mates and also commands respect on and off the field. Eben is also well supported by a strong leadership group within the squad.”
Etzebeth is a skilled lineout jumper, strong ball-carrier and fiery competitor in the loose who won the first of 57 caps against England in 2012 as a 20-year-old.
Loose forward Whiteley sustained a groin injury during the France series and initial expectations that he would be out of action for six to eight weeks proved overly optimistic.
He may be available only for the final two rounds of the southern hemisphere championship from late September at home to Australia and world champions New Zealand.
After home and away Tests against the Pumas on successive weekends, the Springboks have a one week break before tackling the Wallabies and the All Blacks away.
Download our app and read this and other great stories on the move. Available for Android and iOS.