Ali hit six fours to remain unbeaten and just short of a debut half-century.
Bhatti collected three fours and two sixes before he was trapped lbw by Morkel.
South Africa stumbled throughout its reply and Kallis' dismissal after he hit five fours and a six left the home team 115-5.
Duminy's measured 49 from 70 balls gave the Proteas a glimmer of hope but offspinner Saeed Ajmal (2-28) and Bhatti snuffed that out.
