Amla (90) and Kallis (84) forged an unbeaten 136-run stand before bad light cut short the play by eight overs.
Opener Alviro Petersen played well for his 64 while skipper Graeme Smith (10) was dismissed cheaply in the 11th over of the day.
James Pattinson (1-53) and Nathan Lyon (1-61) shared a wicket each for Australia.
The luck too went the Proteas' way as Kallis was bowled off a no-ball while Amla was dropped.
Brief scores: South Africa 2 for 255 (Petersen 64, Amla 90 not out, Kallis 84 not out)