Victorious 2014 ICC U-19 World Cup captain could open with Elgar; Phehlukwayo also included in South African 13-man squad.
Kohli, Rahane laid the platform before the bowlers helps India 50-run win over Australia at Eden Garden, Kolkata on Thursday.
England and West Indies second one-day international was abandoned after only 2.2 overs at Trent Bridge.
India are set to tour South Africa for a three-match Test, six-match one-day international and three-match T20 international series beginning January 5.
Angelo Mathews out as Sri Lanka add Sadeera Samarawickrama and Roshen Silva for Pakistan Test.
MS Dhoni will be the 11th cricketer and the first since Sachin Tendulkar if he gets the Padma Bhushan award.
With 30 September 2017 set as the cut-off date for automatic qualification, the Windies now cannot move ahead of Sri Lanka.
Jonny Bairstow scores maiden ODI century and Stokes took three for 43 ensured West Indies suffered a seven-wicket defeat at Old Trafford on Tuesday.
Visitors need to win the five-match ODI series by a margin of 5-0 or 4-0 for direct qualification for the 2019 global event.
MS Dhoni scored 79 runs and took 2 catches with a stumping, while Hardik Pandya blasted 83 and scalped 2 wickets.