Rain halted the tourists' charge on day one with England struggling to 116 for six and on the verge of posting their lowest total since the new regime of Ben Stokes and Brendon McCullum set about transforming red-ball cricket in this country.
While the hosts moved beyond the 141 they scored here against New Zealand in June, Rabada sent Ollie Pope back to the pavilion early and picked up five for 52 to bring England's first innings to an end inside an hour on day two.
Lord's was a sea of red with the home of cricket turning 'Red for Ruth' for the fourth successive year in memory of Sir Andrew Strauss' wife Ruth, who died in 2018.
All eyes were on Pope first up and whether he could lead England to a competitive total when he resumed on 61 not out, but he should have been dismissed from the sixth ball of the morning.
Having confidently pulled Rabada for four earlier in the over, Pope edged to first slip only to watch Sarel Erwee make a mess of the catching opportunity at chest height.
Erwee spilled the first chance, almost clung onto the second and failed to gather at the third attempt in hilarious fashion while falling backwards.
Pope did not cash in though as he played on at the start of Rabada's third over to depart having added 12 runs to his overnight total.
Stuart Broad, lined up for a nighthawk role by captain Stokes during last month's Test with India, did briefly live up to his billing with two fours off Anrich Nortje able to take England past the 141 they managed here in June.
Rabada again proved too good and showed his variation with a slower ball fooling the England number eight, who could only chip a simple catch to the tourists' skipper Dean Elgar at point.
Jack Leach followed team orders in trying to be aggressive and welcomed Marco Jansen into the attack with two boundaries but soon lost his off stump.
It meant James Anderson, fresh from celebrating his 40th birthday, walked out with England on 164 for nine.
Anderson lasted only one ball with Rabada pinning him in front to ensure his name will go up on the Lord's honours board and give South Africa control, especially as their openers safely guided them to 27 for none at the lunch break.