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Siddle celebrated his 26th birthday in style by dismissing Alastair Cook, Matt Prior and Stuart Broad in successive deliveries after tea as England collapsed from a strong position at 197-4.
In reply Australia were 25-0 at stumps, with Simon Katich and Shane Watson on 15 and nine respectively.
Siddle, who was surprisingly selected ahead of Doug Bollinger for his first Test in ten months, earlier halted England's momentum in the second session when he took the wickets of dangerman Kevin Pietersen and Paul Collingwood, both nicking to the slips, in the space of 11 balls.
He reaped rewards for a probing line outside off stump after tea getting Cook to edge to Shane Watson at first slip after a patient 67. Then Prior was late trying to prod the ball through the leg side and saw his off stump uprooted.
And on the hat-trick ball, Stuart Broad was caught on the toe from a full delivery to make Siddle the 11th Australian to grab a Test hat-trick and the fifth of his countrymen to do so in England-Australia conTests.
Broad challenged the decision, and - after the initial roar from home fans and celebrations on the pitch - there was a delay until the hat trick was confirmed by the TV umpire.
Graeme Swann also fell to the same bowler being caught on the pad playing across the line. Four balls later, Brad Haddin could have completed a seventh wicket for him but diving to his left he dropped James Anderson.
The day began in a dramatic fashion when England captain Andrew Strauss, after winning the toss and electing to bat on a slow Gabba pitch, was dismissed without scoring from the third ball of the day, caught by Mike Hussey at third slip off the bowling of Ben Hilfenhaus.
Midway through the first session Jonathan Trott was bowled for 29 between bat and pad by a Shane Watson delivery that seamed in off the pitch before hitting middle and off stump.
Watson, who was the pick of the Australian bowlers in the morning session, was also unfortunate not to take the wicket of Cook who hit a loose cut shot on 26 to Xavier Doherty in the first session only for the debutant to drop the high chance.
Australia, who had come into this series amid doubts over player form and injuries, were not made to rue this drop, thanks to Siddle's efforts.
The lone bright spot for England on the day was the form of Ian Bell who top-scored with a sparkling 76 before becoming the ninth man to fall when he lofted the ball to Watson at deep point, becoming Doherty's first Test wicket.
Although he failed earlier in his career batting at three, Bell's assured innings and impressive recent form may see him moved back up the order.
Pietersen – booed as the man Australian fans love to hate - looked in good form but again failed to translate a strong start into a big score, extending his run without a century to 27 innings.
Anderson became Doherty's second victim when he was the last man out bowled for 11 while attempting an ambitious reverse sweep.
To complete a fine day for Australia, their openers didn't offer England's bowlers a chance in reaching the close unbeaten.