Clarke missed the final test against India this year and the entire Champions Trophy with a back injury, sparking concerns that he would not be fit for the first Ashes test against England starting at Trent Bridge on July 10.
He made steady progress on his return to the crease, batting for nearly two hours and facing 95 balls for his 45 before he edged a catch through to the wicketkeeper.
Watson, backed by new coach Darren Lehmann to open the batting in the Ashes series, cracked an impressive 90 off 94 balls, including 20 fours.
Australia had reached 240 for four midway through the afternoon session.
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