Doolan's 104 anchored Australia's 273-8 at close on the second day at Sharjah stadium but top-order including Clarke did not get the much-needed practice.
Pakistan 'A' had declared their first innings at their overnight score of 305-8 with skipper Asad Shafiq remaining not out on 108.
Clarke, who is recovering from a hamstring injury sustained on the tour of Zimbabwe in August, looked well set during his 31-ball stay of 10 runs before being caught at point off paceman Ehsan Adil.
But Doolan in company of Steven Smith (58), man-of-the-series in Australia's 3-0 rout of Pakistan in the preceding one-day series, added 106 for the fourth wicket before both retired to give other batsmen some practice.
Doolan's 194-ball innings had 12 boundaries and three sixes as he looked set to keep the Test place he won earlier this year on the South Africa tour.
Smith hit nine boundaries during his 123-ball stay.
All-rounder Mitchell Marsh, also recovering from last month's hamstring injury, failed with a three-ball duck.
The second Test starts in Abu Dhabi from October 30.
Brief scores:
Pakistan 'A' 305-8 dec (Asad Shafiq 108 not out; S. O'Keefe 3-76).
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