Amla was unbeaten on 90 and Jacques Kallis remained on 84, with South Africa unable to add to its overnight total of 255 for two due to persistent rain in Brisbane.
It was the first full day lost due to rain in a test match at the Gabba ground since Nov. 29, 1983, the last day of the drawn match between Australia and Pakistan.
The South African players left around lunchtime to return to their hotel, while the Australians stayed to sign some autographs before stumps was officially called shortly after 4 p.m. local time. The covers did not come off the wicket square all day.
It was a day for the South Africans to regroup after JP Duminy was ruled out of the series after rupturing his left Achilles tendon in a freak training accident after play on Friday. He had surgery on Saturday and could be sidelined for up to six months. His replacement for the remainder of the series is expected to be announced next week.
"It's disappointing,'' South Africa coach Gary Kirsten told the Australian Broadcasting Corp. "He's been playing some really good cricket batting at No. 7 for us.''
Without a specialist spinner in the starting XI, Duminy was expected to play an important role with his offbreak bowling. Now South Africa not only has no spinner, but it has only 10 batsmen available.
With Amla and Kallis rarely troubled in a 136-run third-wicket partnership on day one of the three-test series, the South Africans will be confident of batting for most of day three. Amla scored centuries in both tests in last year's drawn series against Australia in South Africa and is coming off a prolific series against England.
"We would like to get somewhere around 500,'' Kirsten said, "but we've got a lot of work to do and we have to make sure we stay humble and play every hour importantly.''
Australia coach Mickey Arthur said his team's focus was only on getting seven wickets on Sunday, when rain showers are on the forecast. The Australians haven't lost a test at the Gabba since 1988, but are hosting South Africa at the Brisbane venue for the first time in 49 years.
"There's been a huge chunk of the game taken away,'' Arthur said. "We've still got to play very, very well to give ourselves an opportunity to: a) win it; and if we can't win it, b) make sure we don't lose it.''
Australian quicks Peter Siddle, Ben Hilfenhaus and James Pattinson came into the match desperate to challenge test cricket's leading pace trio of Dale Steyn, Vernon Philander and Morne Morkel, but fell into the trap of bowling too short on a Gabba pitch that was moist underneath and unusually slow and lacking sideways movement.
"Probably wasn't good enough,'' Arthur said of Australia's opening day. "We got our lengths wrong. We weren't bad, but we weren't as clinical as we had been, or hoped to be.
"We weren't able to put South Africa under pressure for long enough. On our report card, probably a bit disappointing. We've still got that second new ball up our sleeve – that's the one trump we have. We have to make that second new ball work for us.''