Ali's injury has the potential to put an early end to the 36-year-old's unexpected Ashes campaign.
Moeen was visibly in discomfort, with England's medical staff to continue to monitor the bowler's issue ahead of day two.
Ali, who is likely playing in his farewell Test, remains a key player for England as it looks to tie the series at 2-2. Despite Australia already retaining the Ashes, the importance of a series result remains at the forefront of the minds of the English side.
The off-spinner was called out of retirement leading into summer as a result of an unfortunate injury to the in-form Jack Leach.
Moeen's decision to continue raised concerns that he might be aware that his chances of bowling the final Test were slim. He immediately switched into an attacking stance, scoring 23 runs from the next nine deliveries.
Harry Brook, who combined with Moeen for a 111-run partnership, spoke on the interaction they had after the injury.
"That was his decision really," said Brook.
"As soon as the physio left the pitch he was like 'should I just tee off now' and I said 'you should've been doing that from the start'.
"He is one of the best power hitters in the world and we have seen that in franchise cricket and white-ball cricket.
"Obviously he was in a fair bit of pain ... hopefully later in the game he might have a bit of a role to play."
Given Moeen is ruled out of bowling, the home side is likely to rely on former captain Joe Root to carry the load, a role he embraced earlier in the series.
Australia is currently looking sharp at 1/61 after an eventful first day that saw both sides have their moments.
Although the touring side was able to bowl out their opponents for 283 runs, a handful of dropped catches cast an overhanging cloud on what was an impressive bowling display.