The young South Africans, batting first, made 255-9 in their 50 overs and much of that was down to Rowles, who went to the crease with the score at 1-2 in the second over.
The batter hit six fours and seven sixes in his 109, which was supported by Paul James (46), Armaan Manack (26) and Daniel Bosman (26).
In reply, Australia were motoring towards the target thanks to a blistering 47-ball 85 from opener Will Malajczuk, but their innings was paused on 122-2 after 17 overs.
Both sides start their global tournament on Friday, with Australia facing Ireland and South Africa opening up against Afghanistan.
The South Africa U19s suffered a big defeat in the third and final youth ODI against India, going down by 233 runs as the visitors completed a clean sweep in the 50-over games in Benoni.
The South Africa U19s fell to a series defeat in the youth ODIs against their India counterparts after losing the second game by eight wicket (DLS) in a rain-affected encounter in Benoni.
South Africa's Jorich van Schalkwyk became the first batter in youth ODI history to score a double century as U19 began their tri-series with a thumping 278-run win over hosts Zimbabwe in Harare.
