Hashim Amla (picutured) and Aiden Markhram will want to put on a big score after lunch for the Proteas. Photo: @OfficialCSA via Twitter

CAPE TOWN South Africa lost opener Dean Elgar before lunch but continued to drive home their advantage on the third day of the third test against Australia on Saturday, the hosts reaching the interval on 65 for one in their second innings, a lead of 121.

After Elgar departed, Aiden Markram (36) and Hashim Amla (15) put on a patient partnership of 37 for the second wicket in gloomy conditions, and the pair will look to solidify South Africa's dominant position following the break.

Elgar, who carried his bat for an unbeaten 141 in the first innings, could not repeat that feat as he edged seamer Pat Cummins to Steve Smith at slip for 14.

The catch was the sixth of the match for the Australian captain, who is now two shy of the test record for an outfield player currently held by India's Ajinkya Rahane.

Setting a target of anything over 250 will be a challenge for the Australians, though they did successfully chase down 331 at Newlands in 2002, but on a much more placid surface and with a more experienced top seven.

South Africa had earlier wrapped up Australia's first innings when Kagiso Rabada (4-91) had final man Josh Hazlewood (10) caught by Hashim Amla at first slip.

The visitors had added 10 runs to their overnight total of 245-9 to be dismissed for a deficit of 56 on the first innings.

Morne Morkel, who passed 300 test wickets on Friday, returned figures of 4-87 in what is likely his penultimate test before retirement, while Vernon Philander posted 2-26.

Tim Paine was left stranded on 34 not out, with opener Cameron Bancroft top-scoring in the innings with 77 as Australia's wait for a first century in this series goes on.

The four-match series is poised at 1-1, with the final test to be played in Johannesburg starting on Friday. 

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