Ali, who didn't play in the first Test in Perth, will miss the rest of the series in Australia after undergoing surgery in Melbourne on Saturday.
"Noman Ali complained of sudden and severe abdominal pain yesterday, leading to examinations and scans in emergency that confirmed a diagnosis of acute appendicitis," a Pakistan team statement read.
"Post-surgery he is stable and doing fine. He will be discharged later (on Saturday)."
Noman will be replaced in Pakistan's squad by fellow left-arm spinner Mohammad Nawaz, who will arrive in Australia on "the first available flight" according to a statement late on Saturday from the Pakistan Cricket Board.
Nawaz, 29, had already been named in Pakistan's 17-player T20I squad to take on New Zealand in January.
"Due to logistical challenges, including visa issues for any new player, and considering the requirement for a left-arm spinner, Nawaz was the best available choice for the side," the statement said.
The loss of Noman follows that of fast bowler Khurram Shahzad, who was on Friday ruled out for the remainder of the Benaud-Qadir series.
After impressing on Test debut in Perth last week, Shahzad suffered a stress fracture in his 10th rib, as well as an abdominal muscle tear.
Pakistan travelled to Australia with a weakened bowling line-up after quick Naseem Shah was ruled out due to a long-term injury.
Legspinner Abrar Ahmed missed the Perth Test with discomfort in his right leg, while fiery fast bowler Haris Rauf chose to play in the Big Bash League for the Melbourne Stars instead of appearing in Pakistan's squad.
It left star quick Shaheen Afridi, 23, to carry a heavy load.
Pakistan have lost their past 15 Tests in Australia, last winning back in 1995 at the SCG, with the second match of the series to get under way at the MCG on Boxing Day.
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