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Durban: Johnson took two wickets in his first over, then struck Smith with the third ball of his next over to throw the South African innings into disarray after the hosts had fought back earlier in the day, taking the last six Australian wickets for 49 runs, including the last five for four runs in 18 balls.
Kallis made 22 in a 50-run partnership with JP Duminy (28 not out) when Johnson, in the first over of his second spell, struck him on the jaw with a lifting delivery. He was led off the field bleeding.
His replacement, Mark Boucher, was bowled by Johnson off the last ball before tea.
Wickets tumbled on Saturday after rain delayed the start of play by half an hour.
Australia collapsed from their overnight 303 for four to put South Africa right back into the match; but then it was their turn to collapse with their first two wickets falling for no runs in the first five balls.
The left-armed Johnson had Neil McKenzie caught behind then trapped Hashim Amla leg before, with Amla making an unsuccessful referral to the television umpire.
After Smith's injury, AB de Villiers made only three before he was leg before to Ben Hilfenhaus; South Africa crashed to six for three.
Brief Score: South Africa 138/7 (Duminy 73*, Johnson 3-37, AB McDonald 3-25) trail Australia 352 (PJ Hughes 115, SM Katich 108, DW Steyn 3-83) by 214 runs.
