The injured Kallis and debutant du Plessis resumed with South Africa on 273-7 after lunch, and added a quickfire 70 runs before Australia captain Michael Clarke struck after the drinks break on a sweltering day at Adelaide Oval.
Left-armer Clarke, whose orthodox spin has troubled a number of accomplished batsmen, tempted Kallis into a miscued sweep and wicketkeeper Matthew Wade took a simple catch after the ball kissed the all-rounder's glove after thudding into a pad.
With Kallis out for 58, spinner Nathan Lyon coaxed a similar shot from Morne Morkel minutes later and bowled the tall fast bowler middle-and-leg for six.
Du Plessis struck a defiant half-century on debut but was caught at silly mid-on by Clarke for 78 off Ben Hilfenhaus to bring the innings to a close, which gave Australia a commanding 162-run lead.
All-rounder Du Plessis added a valuable 36 runs with spinner Imran Tahir, left stranded on 10 at the earlier than scheduled teabreak, but South Africa face an uphill battle to save the second test with Kallis unable to bowl.
Following Kallis's dismissal, Du Plessis pushed a single past mid-on off Lyon to raise his half-century and was rewarded with a painful strike on the glove from paceman Peter Siddle from the first bowl of the following over.
Kallis secured his own half-century by pulling Clarke over midwicket for four and followed up by bashing a six over the same area.
Peppered with bouncers by Siddle prior to lunch after the Victorian spotted him wincing with pain, Kallis despatched two short deliveries in succession with a pair of imperious hooks.
Siddle had earlier removed century-maker Graeme Smith and AB de Villiers in a fiery spell of 2-7 in the morning, after spinner Lyon had Jacques Rudolph caught.
Ben Hilfenhaus later took the new ball and had Dale Steyn out for one and Rory Kleinveldt for a duck.
It was offspinner Lyon who sparked the rout, however, as he coaxed Rudolph into an ill-conceived drive that went straight to Rob Quiney at cover.
With Rudolph out for 29, Smith was unable to dig in further as Siddle had him caught behind by Wade for 122.
The 31-year-old referred the decision but the video review was upheld and he trudged off the ground fuming.
Siddle then removed De Villiers for one, trapping the wicketkeeper in front, the decision upheld by video review after another referral.
Clarke took the new ball as soon as it came available and threw it to Hilfenhaus who paid his captain back by capturing Steyn and Kleinveldt in quick succession.
Pitching the ball short of a length and swinging it away, Hilfenhaus found Steyn's outside edge and Ricky Ponting completed a comfortable catch at second slip.
Five deliveries later, the Tasmanian workhorse knocked over Kleinveldt's off-stump as the rookie pace bowler attempted to smash the ball over midwicket.
Australia pace bowler James Pattinson left the field before the end of the first session to have treatment for a side strain.