Mason Crane picked a three wicket haul while James Anderson and Chris Woakes shared two wickets apiece as England managed to restrict Cricket Australia XI to 233 for nine following which they stretched their lead to 65 runs at stumps on day two of the tour game in Adelaide.
Bowling around the wicket, Ball turned his back foot in his delivery slide and fell to the turf, before being helped from the field less than 10 minutes before the first adjournment in play.
Ball collapsed on the pitch and was surrounded by concerned team-mates as medics hurried onto the field.
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England will assess Ball over the next 24 hours in the hope his injury is not as bad as first feared.
The incident comes just two days after Ball's fellow seamer Steven Finn had to leave the Ashes tour with torn knee cartilage to be replaced by the uncapped Tom Curran.
All-rounder Moeen Ali is also missing the four-day match with a side injury.
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England were already without Ben Stokes heading into the tour.
The wickets continued to tumble in the second session with the home side losing Carder, Will Pucovski (4) and Jason Sangha (3).
Former Test and one-day global player Paine, who has failed to feature in Tasmania's Sheffield Shield side this season because of Test incumbent wicketkeeper Matthew Wade's move to the state, combined with Matt Short (45) to rescue his side from a precarious 57 for five.
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Durham's Stoneman, Dawid Malan of Middlesex and skipper Joe Root all passed 50 as England closed on 278-8 in a day-night clash being played with a pink ball in a bid to mirror the likely conditions in the second Test at Adelaide in December.