After being set a target of of 438 by Pakistan, who saw Younis Khan (103) become their most prolific Test century-maker with his second of the match, Australia made a dismal start to their chase.
Chris Rogers (23 not out) and David Warner (29) put together an opening partnership of 44, but Australia were 59-4 at stumps on day four and face a major battle to avoid defeat in Dubai.
Alex Doolan were both dismissed without scoring Nathan Lyon and Clarke (3) was also given out leg before, while Steven Smith (3 not out) will return to the crease on Sunday with Australia requiring an unlikely 379 runs to win.
After scoring a century in his previous Test appearance in South Africa in March, Clarke has been hampered by a hamstring problem in recent months.
And the 33-year-old knows he needs time in the middle after making just five runs in two innings in the first Test.
"I read somewhere the other day that I’m short of match practice and that probably sums my form up at the moment," he said. "In the last Test match I played I scored a big hundred for Australia.
"It has been seven months since our last Test match and I've only played one one-dayer in between that time.
"That doesn't make it easier.
"There's no time between now and the second Test match so I have just got to keep working my backside off in the nets and then when I get another opportunity I need to make sure I bat for as long as I can.
"I need to contribute more.
"That's always been my goal as the Australian cricket captain, to make sure I'm leading from the front and scoring plenty of runs.
"I'll probably be in the gym tonight, training and making sure I'm fit and healthy, get back into the nets tomorrow and do some work on my batting."