At lunch Jacques Kallis was unbeaten on 137 and AB de Villiers was not out 32. Australia's bowlers were largely unthreatening under sunny skies and the home team is facing an uphill task at a ground where they have not been defeated in 24 years.
Amla reached his third century in four innings against Australia and his 17th overall with a slashed cut over the slips for four. The top-ranked batsman in Test cricket was given out lbw to Peter Siddle for 104 but was struck high and TV replays suggested the ball was going over the stumps. Surprisingly, hedid not refer Asad Rauf's decision to the third umpire.
Amla, who became South Africa's first triple centurion with an unbeaten 311 against England at The Oval in July, put on 165 runs for the third wicket with Kallis.
Kallis reached his 44th Test century just minutes after Amla's departure. It was his fifth against Australia. The all-rounder is second on the list of all-time century makers, behind only India's Sachin Tendulkar.
His unconquered 137 is the highest score by a South African in a Brisbane Test since Eddie Barlow's 114 in 1963.