He was later found guilty of "inappropriate and deliberate physical contact with a player" by the International Cricket Council (ICC) and will miss the rest of the four-match series.
The 22-year-old, who took 11 wickets in the match, has appealed the decision.
The tweet, which had a video clip of the incident attached, said Smith was equally guilty and had milked the incident.
"Haven't really seen the footage of this incident but by the looks of this ... Steve Smith gave KG (Rabada) the shoulder," it said.
"He could have avoided any contact but to me he is just as guilty. Trying some football skills to get a penalty??? Pity he didn't dive to top it off."
Early on Thursday, however, Philander distanced himself from the comment, saying someone else had posted to his 185,000 followers.
"Waking up this morning to a lot of twitter craziness as my acc got hacked and someone posted a nice little article on my behalf," he posted after deleting the original message.
"Sorry for all the drama or entertainment caused by the looks of it."
The episode is the latest twist in a tempestuous test series that has seen five players punished by the ICC.
In the first test in Durban, security cameras captured a heated argument between Warner and South Africa wicketkeeper Quinton de Kock after the teams left the field for tea on the fourth day.
Warner said the wicketkeeper had made "vile and disgusting" comments about his wife.
Warner was fined 75 percent of his match fee, while de Kock was fined 25 percent. Both were given demerit points.
Rabada was handed three demerit points for the shoulder bump in Port Elizabeth, taking him to eight within a two-year period, which triggered an automatic two-match suspension.
He was also given another demerit point for a send-off of Warner in the second innings.
Australians Nathan Lyon and Mitchell Marsh are the other players to receive fines and demerit points in the series.
The third match in the series, which is level at 1-1, starts in Cape Town on March 22.
(Writing by Greg Stutchbury and Nick Said; Editing by Peter Rutherford)
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