Smith reclaimed the world record for most Test catches at Kingsmead on Sunday, as Australia's bowlers knocked South Africa over for 284 in their first innings.
Australia went to stumps at 0-33 and a lead of 139 runs when bad light again stopped play, with the under-pressure Nic Maddinson not out on 17.
In ordinary circumstances, Australia could lay claim to being on path to victory in the series opener, with a chance to set a big fourth-innings target for the Proteas.
But 45 overs have been lost in this Test to bad light, with play already starting at 9:30am given the early-season schedule and cloud blowing in off the coast.
Extra time has nominally been added on to the end of each day to make up for time lost, but there is next to no chance of a play reaching 5:30pm with a 6pm sunset.
"There's nothing we can do about it," Nathan Lyon said.
"Whether it's cloud or smog, it is playing a role."
A similar situation awaits in the final two Tests in Gqeberha and Cape Town, where play will start at 10am and 10:30am respectively before the sun sets at 6:30pm and 7pm.
New ICC conditions brought in this month allow a pink ball to be used for Tests where light is an issue.
But it must be used from the start with both teams agreeing, and that is unlikely.
"Outside of a day-night Test it has to be a red ball," South Africa batting coach Ashwell Prince said on Sunday.
"Some nations have played a lot more pink-ball cricket than others, so to get both captains to agree is always going to be a challenge."
When the sun was out, it was Smith and Australia's bowlers who shone brightest on day three.
Pat Cummins led the way with 3-54, as he, Lyon, Josh Hazlewood and Mitchell Starc became the first quartet in history to reach 600 wickets in Tests played together.
Smith played a large part in three of those wickets on Sunday, twice showing his wares to anticipate reverse-sweeps and take smart catches at slip off Lyon (2-58).
The first of those removed South Africa's captain Temba Bavuma for three as part of a collapse of 3-15 before lunch, after the Proteas had reached 1-84 at a rapid rate.
And while that was impressive, Smith's second to catch wicketkeeper-bat Kyle Verreynne on 13 was even better.
The former captain again anticipated the shot and moved before Verreynne had struck the ball, before sticking his right hand out catching it one handed.
"He's an absolute freak," Lyon said.
"He's an incredible thinker of the game, but the way he moves and premeditates those types of catches, they're freaky."
Sandwiched between those dismissals was another brilliant catch to dismiss David Bedingham on 49, this time with both feet in the air at second slip off Cummins.
That edge would likely have flown to Matt Renshaw at first slip if not for Smith, but it did help him go back past Joe Root's mark of 220 for most career catches.
A fourth catch then wrapped up the innings and took his person tally to 223, after Keshav Maharaj, Simon Harmer and Anrich Nortje added a crucial 87 for South Africa's final two wickets.
The Proteas also have themselves to blame for their predicament.
While Renshaw's first-innings 190 was a picture of patience and control for Australia in their 390, South Africa lacked exactly that for large parts of Sunday.
After threatening to stabilise the innings from 4-99, Mulder (30) and Tristan Stubbs (32) were both caught taking on short balls from Cummins in the space of two overs.
Marco Jansen then pulled Hazlewood (2-54) to mid off six overs to leave South Africa 8-197.
All eyes will now be on Maddinson on day four, after a 33-ball first-innings duck drew questions around his selection.
He has started positively, hooking his first ball from Jansen for four and flicking Mulder for six just before play was stopped.
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