Usman Khawaja was unbeaten on 138 with Mitchell Starc not out 16 to hold a lead of 48 runs at the Adelaide Oval.
Skipper Steve Smith was run out for 59 in a mix-up with Khawaja during the middle session.
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Australia 307-6 at stumps in reply to S.Africa's 259-9 dec
Australia were 307 for six in reply to South Africa's 259 for nine declared at the close on the second day of the day-night third Test on Friday.