The 30-year-old Steyn featured in the second Test, which South Africa won by an innings and 92 runs on Saturday, despite suffering from a hamstring injury three days before the match.
He showed no signs of discomfort and took four wickets in the match but the team management decided to rest Steyn in the first two matches in Sharjah (October 30) and in Dubai (November 1).
"Steyn is being rested for the first two one-days, and will return back to South Africa before joining up with the squad for the remainder of the series as well as the T20 series," said team manager Mohammed Moosajee.
Star batsman Hashim Amla, who missed the second Test after returning home to attend the birth of his child, is also doubtful for the first one-day.
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"Colin Ingram has been placed on stand-by for Amla, who is still in South Africa awaiting the birth of his second child. Ingram will join up with the squad on Monday morning," said Moosajee.
Moosajee also added that former coach Gary Kirsten will join to help the one-day squad with their batting, confirming that he will spend five days between the second and third one-days in Dubai and Abu Dhabi.
Kirsten then took over as South Africa coach in June 2011 but left the job in June this year.
"We are going into an important phase leading up to the World Cup (2015) so it will be important for us to tap into as many resources available to us as possible," said Moosajee.