Carey forms a three-man leadership group with Aaron Finch at the helm, and he will share vice-captaincy duties with Josh Hazlewood.
Head retains his spot after he impressed in England earlier this year.
National Selector, Trevor Hohns said: “At the top of the order Aaron Finch, Travis Head and Shaun Marsh all retained their spots after making runs in England, but we have also added further depth to our batting stocks.”
“Alex Carey will pull on the gloves full-time to allow Tim Paine to focus purely on captaining the Test team, which includes preparing for next year’s Ashes. Alex provides us with another strong batting option, as he displayed in last year’s Big Bash, and he’s a wonderful young leader to have around the group and out in the field.”
The three-match Gillette One-Day International Series against South Africa begins in Perth at Perth Stadium on November 4, before the second match at Adelaide Oval on November 9.
Australia’s 14-player squad
Aaron Finch (c)
Alex Carey (vc)
Josh Hazlewood (vc)