Ngidi injured his knee while fielding in a Twenty20 International victory over Australia on Sunday and scans have revealed ligament damage.
"He underwent investigations and further assessments with knee specialists upon his return to South Africa, which revealed a significant ligament injury to the right knee," team manager Mohammed Moosajee said in a statement on Friday.
"Due to the significant nature of the injury, he will require a minimum of 12 weeks of rest and rehabilitation to make a successful return to play."
Ngidi has been an important figure for South Africa across all three formats this year, but will not be considered for the matches against visiting Pakistan, which include three tests, five one-day internationals and three Twenty20 fixtures.
The 22-year-old will hope to be back for the visit of Sri Lanka in March, which will serve as the team's final series before the 50-over World Cup gets under way in Britain in May.
Ngidi has a bowling average of below 20 in his four tests and 23.03 in 13 ODIs since making his debut against India earlier this year.
First Published: November 23, 2018, 3:14 PM IST