Clarke came to the wicket with Australia in a spot of bother at 113 for four but the young man was unfazed by the situation as he mixed caution with aggression to score a superb unbeaten 76.
The New South Wleshman raised 51 for the fifth wicket with Andrew Symonds, but hosts ran into further trouble with Symonds and Simon Katich being dismissed in the space of five balls, reducing Australia at a precarious 167-6 in the 35th over.
Clarke was fast running out of partners but continued to up the tempo adding 69 runs in the last 10 overs, 38 of which came in the last five. He was fortunate enough to have found a willing partner in Lee as the duo strung together 54 runs for the eighth-wicket.
Lee made a handy 22 and their partnership allowed them to build a total in the vicinity of 250.
Earlier, Australian skipper Ricky Ponting called the coin correctly and saw the hosts progress at a slow pace unlike the unusual slam-bang style.
Explosive opener and local hero Adam Gilchrist, staging a return to the team after an extended absence through injury, scoring an almost run-a-ball 47, studded with seven boundaries.
Gilchrist in fact did most of the early scoring as as he lost his out of form partner Hayden perish early making only six from 16 balls. Damien Martyn promised a lot before being out for 24.
Captain Ricky Ponting got in eye in and looked good until he fell for 29. Martyn was outfor 24 little later as Australia, were skating on a thick ice at 113-4 mid-way through their innings.
Medium-pacer Abdul Razzaq was the pick of the Pakistan bowlers, finishing with 4-53 while Mohammad Kalil took 2-55 from 10 overs in his One-day debut.