The ODI series between India and South Africa is set to commence on March 12.
Shardul has played in 11 ODIs and 15 T20Is in which he has claimed 33 scalps.
Thakur got injured on his Test debut against West Indies and had to go through the rigours of rehabilitating.
Thakur has been under the pump as far as his team selection based on his secondary skill-batting is concerned.
India allowed the Black Caps to reach 273 for 8 in 50 overs despite having them at 197 for 8 in the 44th over.
Kapil also said the team selection should never be picked on the basis of liking or disliking.
The selection of Jadhav on the basis of 'he can bowl a bit' and Shardul on the basis of 'he is a handy lower-order batsman' in Hamilton was a glaring but unfortunate testimony of that mindset.
Shardul conceded 80 runs in his nine overs.
Bumrah was almost unplayable and returned with the figures of 3/12 in his four overs.
Thakur's final over took the Wellington T20I into the Super Over.