Sussex quick Archer headed back to Britain on Tuesday in a bid to regain full fitness after a sore right elbow saw him miss the final three Tests of England s 3-1 series win over the Proteas.
The injury has raised doubts over the 24-year-old World Cup winner s availability for England s Test tour of Sri Lanka in March.
Archer played just one Test in South Africa, with his five-wicket haul at Centurion unable to prevent a Proteas win by 107 runs in the series opener before England bounced back.
He will be replaced for the T20s by Lancashire paceman Saqib Mahmood, who was already a member of a separate squad for the upcoming one-day international series.
England had long planned to rest Archer, together with fellow World Cup winners Jos Buttler, Ben Stokes and Mark Wood, from the three-match ODI series in South Africa starting at Cape Town on February 4.
The Newlands match is set to be England s first ODI since they beat New Zealand in a thrilling Super Over final at Lord s last year to clinch a maiden men s World Cup title.
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