'Serious blow' for the touring side after Atkinson leaves the field with a hamstring injury.
The pace bowler increased the injury concerns plaguing England after leaving the playing area early on day two in the Melbourne Test in the Ashes series.
The right-arm seamer felt a problem in his left leg post-delivery of the fourth over during the morning session.
The England team reported the 27-year-old had experienced "tightness" and would spend time on the sidelines for further assessment "in the coming hours".
The final Test of the tour beginning on 4 January gets underway on Sunday, 4 January.
England have previously lost key quicks Mark Wood to a knee injury and another paceman because of a side injury during this series.
A replacement bowler was brought into the squad as injury reinforcement.
His form was underwhelming early in the series, claiming a mere three wickets.
He was left out from the previous Test, before being recalled for the Boxing Day match in the playing XI.
The county bowler improved at the MCG, taking two wickets with the ball, and scoring 28 runs with the bat being one of only three England players who passed ten runs.
Following a brief spell late on the first day, he resumed on Saturday morning and removed Scott Boland taken by the wicketkeeper.
However, at the end of that over, he sent down a variation to Travis Head and suddenly grabbed at his leg.
The English bowler was recalled for the Boxing Day Test following his omission the previous Test.
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