Clarke, who has been plagued by a chronic back problem throughout his career, returned to lead Australia in Harare after a spell on the sidelines with a left hamstring strain.
The 33-year-old duly top-scored with 68 not out in a total of 209-9, but spent several overs off the field before returning for the final over of the innings.
Cricket Australia's official website subsequently confirmed Clarke had suffered an "aggravation" of his hamstring injury.
Somewhat predictably, Clarke did not take to the field for the start of Zimbabwe's reply.
However, he did return to assume leadership duties later in the innings.