The hero of the Hobart Hurricanes' maiden BBL title in January, Owen has made an immediate impact at T20 level for Australia since debuting in the West Indies last month.
Set to make his ODI debut, Owen will have to wait after being ruled out of the third and final T20, as well as the 50-over series against the Proteas.
The 23-year-old passed an on-field assessment, but later displayed delayed symptoms of concussion.
Owen has been placed into the 12-day concussion protocols, ruling him out of the three-match ODI series in Cairns and Mackay.
Batting allrounder Matt Short and injury-prone quick Lance Morris will also miss the ODI series, giving Aaron Hardie and Matthew Kuhnemann a reprieve.
Short has been struggling with a side injury suffered ahead of the T20 series in the Caribbean, but will continue managing that to get it right for the start of the domestic summer for Victoria.
Western Australian speedster Morris has had another setback, sent home to investigate some lower back soreness.
The 27-year-old has been in and around the Australian squad for about three years, but has been limited to just three ODIs so far in his international career due to injury, form and the country's strong fast-bowling depth.
Australia won the first T20 in Darwin, but South Africa hit back in the Northern Territory capital on Tuesday night to level the series.
The T20 decider will take place in Cairns on Saturday night, before the ODIs get underway next Tuesday.
8°C