Cricketers with the likes of Jofra Archer, Jos Buttler, Ben Stokes and Mark Wood will all be rested when England play their first ODIs since beating New Zealand at Lord's on July 14.
Test captain Joe Root is in the ODI squad but hasn’t been considered for the three T20s.
Worcestershire seamer Pat Brown, Somerset batsman Tom Banton and the Lancashire duo of Matthew Parkinson and Saqib Mahmood are included in the ODI squad for the first time.
Banton and Mahmood are among five players who were in the T20 squad for England's 3-2 victory over New Zealand in November but are dropped for the three T20s in South Africa from February 12-16. Sam Billings, Lewis Gregory and James Vince also miss out as World Cup winners Archer, Buttler, Stokes and Wood return to England action.
The ODIs are on February 4, 7 and 9 while the T20s start 12, 14, and 16, all following the conclusion of the four-match Test series, which starts on December 26.
England squad for three ODIs in South Africa:
Eoin Morgan (Middlesex) captain, Moeen Ali (Worcestershire)Jonny Bairstow (Yorkshire), Tom Banton (Somerset), Pat Brown (Worcestershire), Sam Curran (Surrey), Tom Curran (Surrey), Joe Denly (Kent), Chris Jordan (Sussex), Saqib Mahmood (Lancashire), Dawid Malan (Yorkshire), Matthew Parkinson (Lancashire), Adil Rashid (Yorkshire), Joe Root (Yorkshire), Jason Roy (Surrey), Chris Woakes (Warwickshire).
England squad for three T20s in South Africa:
Eoin Morgan (Middlesex) captain, Moeen Ali (Worcestershire), Jofra Archer (Sussex), Jonny Bairstow (Yorkshire), Jos Buttler (Lancashire), Pat Brown (Worcestershire), Sam Curran (Surrey), Tom Curran (Surrey), Joe Denly (Kent), Chris Jordan (Sussex), Dawid Malan (Yorkshire), Matthew Parkinson (Lancashire), Adil Rashid (Yorkshire), Jason Roy (Surrey), Ben Stokes (Durham), Mark Wood (Durham).