All Black McAlister out for two months
New Zealand international McAlister only joined Clermont on loan from Toulon less than two weeks ago to help cover an injury crisis that has deprived the French Top 14 champions of flyhalves Camille Lopez and Patricio Fernandez, as well as versatile Scotland scrumhalf Greig Laidlaw.
But 34-year-old McAlister was forced off 12 minutes from the end of only his second match for the club, Sunday's laboured 35-26 victory over newly-promoted Agen.
The former Toulouse flyhalf, who won 30 New Zealand caps, will "undergo an operation in the coming days".
Clermont travel to London on Sunday to face the team that beat them in last season's Champions Cup Final, denying them a first continental title.
Both teams won their first two Group B matches, although reigning champions Saracens lead by a point having claimed two bonus points to one.
Second-placed Clermont are already deprived of Lopez due to a broken ankle and Fernandez from a dislocated knee-cap, while Laidlaw has a broken leg.
It leaves Clermont sporting director Franck Azema with two options: either move experienced scrumhalf Morgan Parra, who can play at flyhalf, to No.10 or play South African-born France international fullback Scott Spedding there, as he did on Sunday after McAlister's injury.
But having already used up their "joker" by signing McAlister, Clermont cannot bring in another injury replacement.
Clermont face crucial back-to-back home and away clashes with Saracens over the next two weekends, knowing that they must take something from the games to keep alive their hopes of reaching the Champions Cup quarterfinals.
Laidlaw and Fernandez are expected to come back in early 2018 while Lopez is unlikely to be available until March.
Meanwhile, Clermont also announced on Monday that New Zealand international fullback Isaia Toeava and Australian lock Sitaleki Timani have signed contract extensions until the end of the 2019/20 season.
Toeava has won 36 All Blacks caps while fellow 31-year-old Timani has played 18 times for the Wallabies.
"Since they joined Clermont their application has been impeccable and they've had a huge impact on our play," said Azema.
"Between the versatility of Ice [Toeava] and the physical impact Sita [Timani] brings, we're delighted to be able to keep hold of these two players."