Ngidi has been diagnosed with a "significant Grade 1 hamstring muscle tear", which he picked up during warm-ups ahead of the Mzansi Super League play-offs, Cricket South Africa confirmed on Sunday.
"He will commence his rehab and return to play in January 2020, and based on his progress, a decision will be made regarding his availability for selection for the Proteas team," Manjra added.
The Proteas are scheduled to play four Tests, three ODIs and three T20Is. The first Test will start on December 26 in Centurion which will be preceded by two practice matches.