The hosts handed a debut to wicketkeeper batsman Quinton de Kock, one of three changes in the side from the first test.
De Kock replaced all-rounder Ryan McLaren and will bat at number seven, while Dean Elgar will open the innings in place of Alviro Petersen, who is ill.
The Proteas also opted to go with a four-prong pace attack, dropping spinner Robin Peterson for left-arm seamer Wayne Parnell. JP Duminy will be the part-time spinning option.
De Kock, who was handed a central contract by Cricket South Africa on Tuesday, has not played test cricket before but is a rising star in the 50-over format and scored centuries in three consecutive innings against India in December.
"Obviously there will be something in the wicket this morning, but we want to post a decent total and get off on a good note," Smith said at the toss.
Australia captain Michael Clarke, who named an unchanged starting XI, admitted he would have batted first too, but said they will hope to use the overcast conditions to make early inroads into the home line-up.
"The wicket looks good, would have liked to bat first, but hopefully in the overcast conditions we might get some swing early," Clarke said.
The tourists won the first test by 281-runs in Pretoria. The third test will be played in Cape Town from March 1.
Teams: South Africa: Graeme Smith (captain), Dean Elgar, Hashim Amla, Faf du Plessis, AB de Villiers, JP Duminy, Quinton de Kock, Wayne Parnell, Vernon Philander, Dale Steyn, Morne Morkel
Australia: Chris Rogers, David Warner, Alex Doolan, Michael Clarke (captain), Steve Smith, Shaun Marsh, Brad Haddin, Mitchell Johnson, Peter Siddle, Ryan Harris, Nathan Lyon
(Reporting by Nick Said; editing by Sudipto Ganguly)
