Warner left the field to receive treatment on a shoulder injury and had only just returned to the field when du Plessis sent Australia in to face the final 12 overs of the day.
Warner was ruled ineligible to bat for Australia for the opening six minutes of the home team's innings because of his time off the field.
du Plessis says he only though about springing the trap when he overheard Steve Smith register his concern about Warner's availability with umpires Richard Kettleborough and Nigel Llong.
"I was aware of it," du Plessis told ABC Grandstand.
"I saw them speaking to the umpire and I put my ear a little closer towards them and as soon as I heard that he was in trouble with the time I ran off."
The fill-in skipper's leadership received a glowing endorsement from the Channel 9 cricket commentary team.
"I tell you what, it's another big tick for Faf du Plessis with his captaincy," Aussie Test legend Shane Warne said.
"I reckon he's worked that out. He knows that David Warner stayed off the field for too long and he's declared at 9/259 to try and eek out some extra runs.
"Australia have missed a trick and South Africa, they're right on the ball."
Aussie quick Josh Hazlewood said after the day's play he expects Warner to apologise to teammates over the incident.
"The guys were a little bit annoyed, especially Smithy and probably Uzzie who had to go out and bat," said Hazlewood.
"He went off for some treatment towards the end and was off for obviously too long and that messed the timings up and he couldn't bat straight away.
"It's just one of those things. It rarely happens but it happened today. I think Uzzie, the way he adapted to the situation he did a great job for us today.
"(Warner) will hold himself accountable, that's how Davey goes. He knows he did the wrong thing and (will) apologise to the group, learn from it and hopefully it doesn't happen again."
Former Aussie Test opener Michael Slater said Warner threw teammates Usman Khawaja and Matt Renshaw under the bus with his mistake.
"Faf du Plessis is always thinking," Slater said.
"Maybe he knew that and that's why he's declared.
"This is unnerving for Khawaja. It's a different role. David Warner would have been talking to Renshaw this week to get used to each other and try to form a partnership with the work they've done. Now he's not walking out there with the debutant. That throws the whole top order out."
NATHAN LYON HITS NEW LOW
Nathan Lyon's run of 110 first class overs without taking a wicket were finally ended when Aussie keeper Matthew Wade pulled off a brilliant stumping of Kagiso Rabada.
The off-spinner hadn't claimed a scalp since South Africa's first innings of the first Test in Perth.
Across Tests and first class cricket Lyon had bowled 0/407 runs from 660 deliveries.
He was also 0/234 since his two wickets on day one at the WACA.
Aussie Test great Shane Warne said Lyon would be worried with his form, while former Australian Test skipper Mark Taylor said Steve Smith had again poorly utilised his spinner by bringing him on to bowl too late.
DU PLESSIS SHOCKED BY ADELAIDE HOSTILITY
Controversial South African captain Faf du Plessis was booed by the Adelaide Oval crowd on his way out to bat.
With the Australian bowlers well on top in the opening session of the Third Test, du Plessis walked out to bat with his team 3/44.
After he was found guilty of ball tampering and fined his entire match fee following the second Test, the Adelaide crowd let the Proteas skipper have it.
As du Plessis walked onto the field, the normally reserved Adelaide Oval crowd, including its members' section, erupted.
The skipper maintains he's innocent, despite being found guilty by the International Cricket Council (ICC).
The crowd let du Plessis have it again in his second over out in the middle when he defended a ball and proceeded to pick it up to return it to the Australian fielders.
The Adelaide crowd then gave a loud appeal and continued to heckle du Plessis for handling the ball.
He went on to make 118 not out in an innings he described as his most memorable knock.
He admitted he was caught off guard by the response from fans.
"I was expecting a bit of hostility but not to that extent," he said.
"When I got to 100 I wasn't expecting to still get booed. It's pretty disappointing.
"It was my best (hundred). Because of the week and everything that was required to get to this point where I'm sitting now. In the context of everything, it's the best.
"I'm really proud of today. It was a big day for me to stand up as a captain and make sure I lead from the front. I was extremely motivated today... I felt it was a real character test... I was so driven I felt like I could have batted for a week."
'GET YOUR HANDS OFF THE BAGGY GREEN'
KEVIN Pietersen and Ian Healy have called for the end of the trend of smothering teammates for performing well in the field.
The Channel 9 commentators said they felt for Matt Renshaw when the Australian team ran towards the Aussie debutant and proceeded to batter him around the noggin for taking his first Test catch.
Renshaw took a good catch at first slip falling to his right to remove Hashim Amla off the bowling of Josh Hazlewood.
"Why is it as soon as you do something for the first time in an international side everyone just rips your hair apart and tries to take your hat off," Pietersen asked during his television commentary.
"You always see it don't you. I don't know where this started. There, they just rip it off. Why do they do it?"
Healy said he didn't like the way Renshaw's baggy green cap was unprotected during the barrage from his teammates.
"It's just to belittle everyone," Healy said.
"Belittle the recipient of a great piece of work. Get your hands off the baggy green. A sweaty bowler is the last person you want touching your baggy green."
