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Morkel, 32, last played in an international match in June and since then has struggled with a persistent back injury which threatened to end his career.
He was part of South Africa's Test tour of Australia in October and November last year but his injury flared up again after he played in two warm-up matches.
New Zealand-South Africa fourth ODI moved to Hamilton
The tall fast bowler has undergone extensive rehabilitation and returned to action in a domestic one-day game last week.
"Morne Morkel has worked hard on his fitness over the past few months and we believe he is now 100 per cent fit and fully able to compete for his place in the team," said selection convener Linda Zondi.
Morkel, who achieved his Test-best figures of six for 23 in Wellington on South Africa's previous Test tour of New Zealand in 2011/12, is one of six fast bowlers in the 16-man squad. Left-armer Keshav Maharaj is the only specialist spinner.
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There are two uncapped players in batsman Theunis de Bruyn and wicketkeeper Heinrich Klaasen.
De Bruyn was in the squad for a home series against Sri Lanka earlier in the season but did not play, while Klaasen, 25, replaces Dane Vilas as reserve wicketkeeper after Vilas signed a Kolpak contract to play county cricket in England.
Seven of the players are already in New Zealand for a one-day series. The other nine will depart on Saturday.
Squad:
Faf du Plessis (captain), Hashim Amla, Temba Bavuma, Stephen Cook, Theunis de Bruyn, Quinton de Kock (wkt), JP Duminy, Dean Elgar, Heinrich Klaasen (wkt), Keshav Maharaj, Morne Morkel, Chris Morris, Duanne Olivier, Wayne Parnell, Vernon Philander, Kagiso Rabada.
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