India were 76 for one at lunch after winning the toss and batting on what looked an easy-paced pitch.
Morkel claimed South Africa's only wicket when he had Shikhar Dhawan caught at third slip off the first ball after the mid-morning drinks break.
Dhawan made 39 in an opening stand of 41 with Murali Vijay. Vijay was unbeaten on 33 at lunch.
Morkel suffered a sprained right ankle while fielding on the third day of the drawn first Test in Johannesburg last Friday.
It was initially expected he would be out of action for between seven and ten days but he passed a fitness test on Thursday morning after intensive treatment.
Dhawan and Vijay both looked confident at the start of the innings and the left-handed Dhawan struck four boundaries before edging a drive to Alviro Petersen at third slip.
India made one change, with left-arm spinner Ravindra Jadeja replacing off-spinner Ravichandran Ashwin.
South Africa also made a change of spin bowlers, with left-armer Robin Peterson coming in for leg-spinner Imran Tahir.
Jacques Kallis led the team on to the field to a standing ovation from the crowd after announcing on Wednesday that he will be retiring from Test cricket after the current Test.
Kallis is playing in his 166th Test match in a career which started in 1995/96.