The pace bowler, who burst on to the scene in stunning fashion in 2019 and played a key role in that summer's World Cup triumph, has not played international cricket since March 2021 due to injury.
The 27-year-old suffered a sequence of elbow problems, requiring two operations, and then saw his return to action fall apart when he sustained a stress fracture of the lower back in May.
But he has worked closely with the England and Wales Cricket Board's medical team throughout his lengthy rehabilitation and joined up with the Lions squad during November's training camp in November.
He bowled nine overs against the senior England team during their warm-up match in Abu Dhabi, hitting a good pace and raising hopes that he was close to full fitness.
Archer takes his place in a 14-man squad for the three-match tour of South Africa, a rearranged series that was initially abandoned in December 2020 after a Covid-19 scare saw England fly home early.
Harry Brook's surge to prominence continues with his first ODI call-up, with the Yorkshireman fresh from a starring role in the historic Test victory in Pakistan and the T20 World Cup win.
The 23-year-old has been an ever present on England's hectic winter schedule but has not been rested ahead of the Test trip to New Zealand in February, while others such as Mark Wood and Joe Root do sit out. Ben Duckett, who won the last of his eight 50-over caps in 2016, also returns to the fold having re-established himself in the T20 and Test set-ups over recent months.
Reece Topley, who was ruled out of the T20 World Cup after tripping on a boundary sponge, is also involved but Liam Livingstone is out with the knee injury he suffered on Test debut in Rawalpindi.
Sam Billings, Liam Dawson, Chris Jordan, James Vince and Luke Wood all featured in the most recent ODI squad in Australia but are absent this time.
England's ODI squad for South Africa: J Buttler (c, wk), M Ali, J Archer, H Brook, S Curran, B Duckett, D Malan, A Rashid, J Roy, P Salt, O Stone, R Topley, D Willey, C Woakes.