South Africa were able to beat the bat with fair regularity in the opening hour, but battled to create clear-cut chances, with Philander (one wicket for five runs in 7.4 overs) having two appeals for lbw turned down.
Rabada was reported for an incident that happened in the eighth over of India's innings.
Australia vice-captain David Warner has said a "vile and disgusting" sledge about his wife from South Africa wicketkeeper Quinton de Kock was the trigger for his angry outburst in the players' tunnel during the Durban test.
Shaun Marsh followed in exactly the same mode of dismissal as Smith with Rabada striking him on the pads. Lungi Ngidi (3/51) and Vernon Philander (2/25) supported Rabada well.
"He would leave a massive hole‚" Philander said. "There is a fine line about whether you celebrate too hard". The International Cricket Council takes a dim view of any unnecessary physical contact on the field. "That's what we are here to do", Smith said on Tuesday, via ESPNCricinfo.
"I've got full respect for those guys and no doubt they'll make the decision they think is worthy".
Rabada now has five demerit points to his name, having picked up a third sanction by the ICC in the past 12 months with his send off of India's Shikhar Dhawan in the fifth match of their one-day series last month. He would incur another ban if he picked up another demerit point.
Warner admitted the offence and accepted the sanction proposed by Jeff Crowe of the Emirates Elite Panel of ICC Match Referees, according to an ICC statement.
After getting Marsh out on the second ball of the 54th over, Rabada struck twice more in successive deliveries as he took out Mitchell Marsh and Pat Cummins on the fifth and sixth balls respectively. In contrast to the first day, the weather was bright and sunny and the pitch appeared to be offering less help to the seam bowlers.
Previous year he was found guilty of deliberate physical contact with Sri Lanka's Niroshan Dickwella and was given three demerit points. He scored his runs off 100 balls with nine fours. Smith and Shaun Marsh put on 44 before Rabada's day-changing spell, when Australia tumbled from 161-3 to 182-8.
Rabada took three of his wickets in an over, and removed Australian batsmen on the last ball before tea and first ball after it, to turn the tide in the home team's favor.
Lyon admitted that Australia's collapse was disappointing but said he was confident they could fight back.