Rabada, who will have his name on the honours board at the venue, ended his first innings shift with 5/51, supported by Anrich Nortjé with three wickets and Marco Jansen with two.
England resumed on day two with on 116/6, but Rabada was in inspired form to claim the wickets of Ollie Pope (73), Stuart Broad (15) and James Anderson (0), with Jansen removing Jack Leach (15).
This means England only added 49 runs to their overnight score in 13 overs inside the first hour of day two as they continued to struggle with the pace of Rabada, Nortje, Jansen and Ngidi, who was unlucky not to get any wickets.
It is now up to veteran fast bowlers Anderson, Broad, Matthew Potts and possibly spinner Jack Leach to try to dismantle this Proteas opening partnership.