Warner was despatched to southern Africa from the tour of England to find some form after being suspended for punching England batsman Joe Root in a bar.
In Pretoria, he reached three figures with his 18th boundary shortly before tea on the opening day of the four-day game.
Batting at number four, he hit 29 fours and a six before being dismissed by the final ball of the day as the tourists reached 399 for five. Glenn Maxwell finished unbeaten on 103.
Australia's top order has failed to fire during defeats in the opening two tests of the five-test Ashes series. Warner is due to return to the squad in time for the third test against England, starting on August 1 at Old Trafford.
He was suspended last month for punching Root in a bar following a Champions Trophy game between the teams.
The 26-year-old was then banned until the first test and was not named in the team for the game. He was deemed "in need of match practice and runs in the longer format" and joined the Australia A tour to Zimbabwe and South Africa.
Australia unveiled another surprise after the selection of Ashton Agar for the first test by picking the 20-year-old off-spinner Ashton Turner for the three-day match against Sussex.
The touring side are resting many of their test players for the game at Hove, which starts on Friday.
Turner, who will be making his first-class debut, has played for the Australian under-19s and joins fellow spinners Ashton Agar and Nathan Lyon in the side.
Agar made his test debut against England at Trent Bridge, scoring 98 in Australia's first innings batting at number 11.
England have asked for James Taylor to be released by Nottinghamshire to play for Sussex in the tour match. Kevin Pietersen may miss the third test through injury and Taylor, who played two tests in 2012, would be a possible replacement.
(Reporting by Nick Said; editing by Robert Woodward)
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