Captain Temba Bavuma will have to undergo a fitness test on Monday to take a final call on his availability.
Ngidi will next play in January, and is likely to take part in the third campaign of the SA20.
On the other hand, Bavuma is in a race to start the two-game series against Sri Lanka that kicks off on November 27 in Durban. He is returning from an elbow knock that kept him out of the contests against Bangladesh last month.
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His loss would be more keenly felt than Ngidi, with South Africa having depth in their seam department but still at times brittle with their top six batting.
South Africa have a chance of reaching the 2025 World Test Championship final but would likely have to win both tests against Sri Lanka, and the two-match home series with Pakistan that includes Boxing Day and New Year fixtures.