Milne sustained an Achilles injury while warming up for Central Districts' Plunket Shield match against Wellington this week. Although it was not considered serious, the New Zealand medical team did not want to risk further injury and recommended Milne remain in New Zealand.
He will undergo a period of rehabilitation and continue to be monitored closely by New Zealand Cricket and Central Districts medical staff.
"It is disappointing for Adam to suffer an injury, however, it does present a great opportunity for Mark," national selection manager Kim Littlejohn said. "Mark has an impressive record in South Africa and the conditions will suit his aggressive style of pace bowling."
The New Zealand squad depart for South Africa in two groups today and tomorrow.
Gillespie has played 11 Twenty20 internationals since his debut against Sri Lanka in 2006 but his last was in 2008. The 33-year-old was recalled to the test side for last summer's series against South Africa after some compelling domestic form but a serious ankle injury scuppered any chance he might have of playing over the winter.
He has played only one T20 game for Wellington this season, when he collected figures of 0-43 off four overs, but has had more success in Plunket Shield with 13 wickets in his three matches to date.
