Clarke's unbeaten 161 helped the tourists push on to 7-494 in their first innings in Cape Town, before rain arrived to force a premature close with only 39.4 overs bowled on Sunday.
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Australia's captain was forced to undergo a testing examination from Morne Morkel on day one, but battled through before completing his 27th Test hundred the following morning.
The century ended a barren spell for Clarke, who was left to ponder the timing of a potential declaration.
"It's obviously very satisfying to contribute in this series. I was overdue," admitted the 32-year-old.
"We have had one-and-a-half days of Test cricket and we have 494 runs on the board, so I am extremely pleased with the position we are in.
"The forecast is pretty good for the next three days. I'll have a good chat to Boof (Australia coach Darren Lehmann) tonight.
"Obviously our goal is to win this Test match, so if that means batting for some time and getting as many runs as we can, if we think it's the best way to win, we'll do that.
"If we think declaring overnight is the best way then it doesn't bother me.
"You've got to sum up runs in your first innings versus how tough they're going to be (to make) in (the) second innings, how much time's left in the game, what the weather's like.
"(There are) a few things to consider, but the most important thing is how you're going to win."
South Africa seamer Kyle Abbott remains wicketless on his return to the international arena, having marked his only previous Test outing against Pakistan 12 months ago with sensational first-innings figures of 7-29.
"I probably bowled a bit worse then actually, but that's the great thing about this game, it humbles you," said Abbott, who insisted the hosts could still claim a series-clinching triumph.
"As soon as we start thinking of a draw or any negative thoughts come in, we won't be on the right track.
"Knowing this team, we're still going to stay positive. There's a series up for grabs."