Ball hurt himself after falling awkwardly just four overs into his opening bowling spell on Thursday, the second day of the match.
Joe Root's side are already without Middlesex bowler Steven Finn, who was forced to fly home earlier this week after sustaining damage to cartilage in his left knee.
Ball is in doubt for England's next assignment, a four-day tour match against a CA XI in Townsville starting Wednesday.
It is the second of England's three tour games before the opening Test in Brisbane starts on 23 November.
Woakes looked unsafe with the pink Kookaburra in his hand and returned figures of 4/17 in ten overs as a young CA XI side slumped to 70/7 chasing 264 runs to win.More news: TPP nations 'have made good progress' on deal, no-show 'a misunderstanding'
An England team statement on Saturday said scans showed Ball had strained ligaments in his right ankle.
The England medical team will assess the injury over the next week and he will play no further part in the match.
Anderson will replace regular vice-captain Ben Stokes as he was withdrawn from the Ashes squad following his alleged involvement in a street brawl outside a nightclub in Bristol. With Moeen Ali, their first-choice spinner, yet to bowl on the tour after suffering a side strain, England's preparations for the first Test at Brisbane remain far from ideal.