Australia were 180 for three at today's tea in Manchester, with Clarke, who won the toss, 55 not out.
Steven Smith, who survived two unsuccessful England reviews as the hosts used up all their challenges for the innings, was 20 not out after so far helping Clarke add an unbroken 51 for the fourth wicket.
The tourists lost just one wicket in the session when opener Chris Rogers, in sight of a maiden Test hundred, was lbw to off-spinner Graeme Swann for 84.
Although Australia had recalled David Warner, usually an opening batsman, they stuck with all-rounder Shane Watson and left-hander Rogers as their first wicket duo.
The pair responded by putting on 76 before Watson was caught at first slip by England captain Alastair Cook for 19 off first change Tim Bresnan after James Anderson, on his Lancashire home ground, and Stuart Broad had seen several good outswingers go unrewarded.
But after 81 minutes Watson, as he is prone to do, pushed firmly forward and edged Bresnan to Cook.
