Rabada, passed fit following an ankle injury, removed openers Alex Lees and Zak Crawley early on during a return of 2-36 in 12 overs.
And Nortje, one of eight South Africans playing their first Test in England, grabbed three wickets, including the scalp of home captain Ben Stokes.
Only Ollie Pope, with an unbeaten 61, offered prolonged resistance before rain arrived half an hour after lunch, turning into a downpour that left the outfield saturated.
Following weeks of searing temperatures in England, Wednesday's bad weather meant only 32 overs were possible before the players left the field early in the second session.
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