Atkinson clutched his upper left leg after bowling the final ball of his fifth over and exited the field soon after in a major blow for England's hopes of a first test win in Australia in 15 years.
Australia were 35 for one in their second innings, having extended their lead to 77 runs, when Atkinson came off, the seamer having had nightwatchman Scott Boland caught behind for six in his previous over.
Australia lead the five-test series 3-0.