James Anderson was particularly innocuous on his home ground, recording his worst Test figures of 0-116 two days after being
described as the best bowler of his era
by Pakistan legend Wasim Akram.
Clarke's declaration 15 minutes after tea gave Australia more than two hours to bowl before stumps and they almost claimed the prized wicket of Cook early on.
A fizzing delivery from spinner Nathan Lyon in his first over of the series grazed the edge of Cook's bat before cannoning off wicketkeeper Haddin's pads and landing just short of Clarke's despairing dive from slip.
Swann congratulates Clarke
Root played with extreme caution to make eight off 57 balls, but succumbed half an hour before the close when he edged Siddle behind.
The seam bowler then had Bresnan caught on the pull. He opted against referring the decision, only for replays to show the ball brushed his thigh.
There was more drama in the penultimate over as Trott called Cook through for a sharp single, leaving his captain at the mercy of David Warner's throw, which came within a whisker of hitting the stumps.
Setting an aggressive tone, he cracked consecutive fours off Anderson followed by three in a row off Tim Bresnan as he and Smith set a new record fourth-wicket partnership at the ground of 214.
Jonathan AgnewBBC cricket correspondent
"I was very disappointed to hear people booing David Warner when he walked out to bat. That kind of behaviour may be acceptable in other sports but it is not what cricket is about.
"On the other hand, Warner did little to enhance his reputation in the England supporters' eyes with his extraordinary decision to review his dismissal after a thick edge that flew off Matt Prior's leg to Jonathan Trott at slip."
He was soon departing to an even louder chorus of boos after penning a whole new chapter in the decision review system sub-plot that is fast becoming a major diversion from the main narrative.
Given out for five to a slip catch off Swann, Warner risked Australia's last remaining referral and was made to look foolish when replays revealed a clear edge on to Matt Prior's pad before the ball looped to Trott at slip.
Australia's leading Test batsmen
Ricky Ponting (168 Tests)
Allan Border (156)
Steve Waugh (168)
Matthew Hayden (103)
Mark Waugh (128)
Justin Langer (105)
Despite the England fans' delight in seeing Warner so embarrassed, there was no shift in the momentum as Haddin attacked the home side's bowling in a sixth-wicket partnership of 62 with Clarke.
Clarke's downfall, gloving Broad on to his stumps, and the castling of an over-ambitious Siddle by Swann, also proved to be momentary blips as Haddin and Starc kept Australia on top with an entertaining unbroken stand of 97 off 118 balls.
Starc, in particular, belied his position at number nine with some straight drives reminiscent of former Australia opener Matthew Hayden and had hit nine fours in his 66 not out by the time Clarke called time on the innings.
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