Rabada shouted in celebration and approached Smith aggressively after winning a leg before wicket decision against him and the shoulders of the players made contact.
However, Rabada may well need to make whatever impact he can quickly, given the possibility of him being suspended for the third and fourth Tests of the series.
He will appear before a hearing tonight.
Rabada finished with five for 96, having done all his damage on either side of tea, taking the key wicket of Australia captain Steve Smith, then following up by dismissing the Marsh brothers - Shaun and Mitchell - in his next over. They were saved from a worse fate when Tim Paine made 36 and put on 61 with Australia's last two batsmen.
"It's that type of wicket where you actually probably never feel like you're in", Lyon said.
South Africa vs Australia 2nd Test Day 2 Live score: Dean Elgar is on 11 at the start of Day 2.
"When you've got a world-class bowler like Rabada bowling in a spell like that, we've got to be better and sharper to identify those big moments and try and shut that down", Lyon said.
Rabada was at it again after the break, Pat Cummins gone for a duck as he, too, edged to De Kock, with Starc only briefly able to stem the flow.
Australia batsman David Warner on Wednesday was fined 75 percent of his match-fee for bringing the game into disrepute on day four of the first Test against South Africa in Durban.
Rabada took 5/96 in Australia's first innings.
Amla, struggling for form after a poor one-day series against India and dismissals for nought and eight in the first Test in Durban, was 31 not out.
Mitchell Starc (8) was Rabada's fifth victim, clean bowled to leave Australia reeling on 182-8.
Tea was taken after Mitchell Marsh was out. Not only did he knuckle down when the wicket was at its most unsafe by scoring just eight off 36 deliveries, he then brought back the real Warner to crack 42 off his next 33.