It was a near-identical replay to the spray he gave Smith, but on this occasion he didn't brush the batsman's shoulder.
Warner, who would have risked a suspension if he rowed with Rabada, walked off.
Umpire Sundaram Ravi was unimpressed with the incident, the latest in a series stacked with bad blood, blow-ups and barbs.
Ravi quickly pulled Rabada to one side, urging him to calm down, then later gave captain Faf du Plessis a lecture.
Similar send-offs have resulted in a level-one sanction in the past.
Crowe read the riot act to both du Plessis and Smith between the first and second Tests, urging the rival captains to improve their teammates' behaviour and play the game in better spirits.
Rabada was then told what he did to Smith was unacceptable by officials, but he appears determined to go out with a bang.
Losing Rabada, who hit the 151 km/h mark on Sunday and snared five wickets in 18 deliveries on Friday, would be a big blow to South Africa's hopes of their first home Test series win over Australia in the post-apartheid era.
The Proteas may opt to rush Dale Steyn, who has started to bowl in the nets after recovering from a heel injury, back into their XI.
Rabada is one of the best fast bowlers in the world but the 22-year-old's white-line fever has already proven costly.
The right-armer missed a Test against England last year because of a send-off of Ben Stokes, while he gave India batsman Shikhar Dhawan a spray in an ODI last month.
Pace legend Michael Holding has already cautioned Rabada about the need to take control of his emotions.
"Kagiso gets a little bit carried away. I have spoken to him a few times about it, to try and get him to relax a bit," Holding told ESPNcricinfo.