South Africa were in a strong position thanks to half-centuries by Kallis (54), AB de Villiers (64) and Ashwell Prince (50), but they lost their way after tea as Australia took six wickets for 25 runs in 11 overs.
The home side were all out in 71 overs, having won the toss and chosen to bat at the Wanderers.
Paceman Peter Siddle claimed three for 69, while spinners Nathan Lyon and Michael Clarke took two wickets apiece as South Africa let a weakened Australian attack off the hook in perfect batting conditions.
The visitors were a man down for most of the day after seamer Shane Watson limped off with a hamstring strain after bowling just 3.5 overs.
South Africa had the bowlers at their mercy as Kallis and Hashim Amla (19) added 80 runs off just 85 balls for the third wicket and their collapse was down to loose strokeplay more than anything else.
Kallis lashed his 54 off just 41 balls before casually flicking Siddle to midwicket.
Amla fell three overs later, edging a slash off debutant Pat Cummins to second slip, before De Villiers and Prince combined to put South Africa back in control with a fifth-wicket stand of 112.
The left-handed Prince began the final-session collapse when he shimmied down the pitch and drove off-spinner Lyon to deep mid-on.
De Villiers fell five balls later as a loose pull shot skied the ball over bowler Siddle's head, Cummins doing well to run backwards and hang on to the half-chance.
Vernon Philander was trapped plumb in front of the stumps by Lyon for a duck and Mark Boucher (3) also fell to an unconvincing pull shot off Siddle.
The floodlights came on and bad light would almost certainly have intervened if Australian captain Clarke had not turned to the slow bowlers.
Clarke himself took the last two wickets - Morne Morkel for six and Imran Tahir for a duck - to claim impressive figures of two for six in four overs.
South Africa captain Graeme Smith had earlier won what seemed a valuable toss and he and opening partner Jacques Rudolph put on a first-wicket stand of 24.
Smith (11) then edged a top-class delivery from left-arm paceman Mitchell Johnson to Clarke at second slip, while Rudolph scored a bright 30 before he edged a catch off Watson to wicketkeeper Brad Haddin.
Kallis played with tremendous authority and a sumptuous cover drive sent his first ball, bowled by Watson, racing to the boundary and drew him level with West Indian left-hander Brian Lara on 11,953 runs.
He then took a single off his third delivery to surpass Lara, leaving only Indians Sachin Tendulkar (15,086 in 183 Tests) and Rahul Dravid (12,979 in 159 Tests) and Australia's Ricky Ponting (12,495 in 155 Tests) ahead of him on the run-scorers' list.
South Africa were unable to bowl a single delivery at the Australians as bad light prevented the visitors from starting their innings before the close.
