Raina has also overcome fitness issues to make the 16-man squad led by Virat Kohli.
The southpaw had played his last international, a T20 against England, in February 2017 before being sidelined with fitness issues.
Passing the mandatory 'Yo Yo' test also paved the way for his return.
He was also in top-form in the recently-concluded Super League of Syed Mushtaq Ali, smashing an unbeaten hundred and a couple of half centuries for Uttar Pradesh.
Familiar faces like Bhuvneshwar Kumar and Shikhar Dhawan were back in the side after being rested for the last T20 series against Sri Lanka.
Rohit Sharma had captained the side in three-match series with Kohli being rested.
The crux of the ODI and T20 squad for the limited-overs leg in South Africa remains the same.
The return of senior players means the likes of Deepak Hooda, Mohammad Siraj, Washington Sundar and Basil Thampi miss out.
All four were part of the home series against Sri Lanka.
Pacer Jaydev Unadkat has been retained after bagging the man of the series award against Sri Lanka while left-arm spinner Axar Patel made a comeback in the shortest format.
Mumbai pacer Shardul Thakur has also been picked after earing a spot in the ODI squad for the six-match series starting February 1.
The three-match T20 series in South Africa begins on February 18 in Johannesburg, followed by matches in Centurion (February 21) and Cape Town (February 24).
India's squad for T20I series: Virat Kohli (Captain) Rohit Sharma (vice-captain), Shikhar Dhawan, KL Rahul, Suresh Raina, MS Dhoni (wicket-keeper), Dinesh Karthik, Hardik Pandya, Manish Pandey, Axar Patel, Yuzvendra Chahal, Kuldeep Yadav, Bhuvneshwar Kumar, Jasprit Bumrah, Jaydev Unadkat, Shardul Thakur.