South Africa were 140 for two in reply to Australia's first innings of 369 when bad light ended play 8.4 overs early.
Kallis was 72 not out with De Villiers on 48 in a stand of 130 for the unbroken third wicket.
They started their partnership after South Africa had slumped to 10 for two in the fourth over.
Michael Hussey, who was last out for 75, shared stands of 56 with Shane Warne for the eighth wicket and 42 with Stuart Clark for Australia's 10th wicket.
Fast bowlers Makhaya Ntini and Andre Nel took three wickets each for South Africa.