Kallis came to the crease with the hosts reeling on 46 for two after being sent into bat and they slumped to 127 for five midway through the afternoon session.
But the experienced all-rounder played a straight bat to everything England threw at him in his 33rd Test century, reaching the close on 108 not out with Dale Steyn on 26.
Wicketkeeper Mark Boucher made a fluent 51 and Steyn also shared a crucial partnership with Kallis before bad light ended play with just over six overs remaining.
England seamers James Anderson and Graham Onions removed Ashwell Prince and Hashim Amla in the morning as South Africa limped to 51 for two at lunch.
Score Board
SOUTH AFRICA (I innings)
Smith* c Prior b Anderson 30
Prince c Prior b Anderson 0
Amla lbw b Onions 14
Kallis (batting) 108
AB de Villiers c Strauss b Swann 36
Duminy c Prior b Swann 0
Boucher lbw b Broad 51
Steyn (batting) 26
Extras (B-1, LB-11, W-1, NB-1) 14
Total (for 6 wkts in 83.2 overs) 279
Fall of wickets: 1-1, 2-46, 3-51, 4-127, 5-127, 6-216.
Bowling: Anderson 20-1-62-2, Onions 18.2-3-60-1, Broad 19-6-54-1, Swann 22-1-74-2, Pietersen 4-0-17-0.
Deccan Herald is on WhatsApp Channels | Join now for Breaking News & Editor's Picks