The pair put on an unbroken 174 for the fourth wicket after opener Chris Rogers set the tone for Australia's first successful batting display of the series with a positive 84.
Drawing on all his expertise against spin bowling, Clarke got the better of off-spinner Graeme Swann in a fascinating duel on a wicket that turned from the start as he posted the first century by any Australian in six Tests.
But once again, in a
series blighted by controversies,
the day featured several contentious umpiring decisions, with both teams given reason to bemoan the decision review system.
After the interval it was England's turn to feel aggrieved. Bowler James Anderson, wicketkeeper Matt Prior and the slips went up in unison to claim a catch off the edge of Smith's bat but umpire Marais Erasmus remained unmoved. Once again Hot Spot showed nothing and the umpire's decision stood.
England used up their second referral when Swann's lbw appeal to Smith was rejected, and were therefore powerless to overturn Tony Hill's decision not to raise the finger when Stuart Broad trapped the same batsman in front of middle stump.
Amid the turbulence, Clarke remained a picture of calm. Purposeful in defence and attack, he drove elegantly down the ground and through the covers and twice crashed the ball over Swann's head for four.
A nibble at an outswinger from Broad that almost caught the edge of his bat was as close he came to offering a chance, and when he brought up his 24th Test century off 169 balls in the evening session he was given a standing ovation by the 25,000-strong crowd.
Clarke's superb innings also helped ease the pressure on David Warner, who was shown on camera fidgeting nervously on the team balcony as he prepared for his first Test innings since he was
suspended for punching England's Joe Root.
Warner's recall was one of three changes for Australia, who brought in off-spinner Nathan Lyon and left-arm seamer Mitchell Starc for Ashton Agar and James Pattinson.
Kevin Pietersen passed a fitness test
to take his place in an unchanged England side.
After Clarke won the toss for the first time in the series, Australia's under-pressure openers put on 76 for the first wicket to lay down an ideal platform for a solid total.
Rogers, twice dismissed softly and cheaply by Swann in
Australia's 347-run defeat at Lord's,
took the attack to the England bowling as he brought up his fifty off 49 balls with his third four in the space of four deliveries from Anderson.
Shane Watson was the first to fall to a fine piece of bowling by Tim Bresnan, who got a ball to shape away from the right-hander, inducing a thick edge to Alastair Cook at slip.
Khawaja had just survived a big lbw appeal by Swann when he drove lavishly at a ball that turned sharply away from him and was given out caught behind by Hill. The batsman instantly sent for a review and looked astonished when it failed to deliver the reprieve he was clearly expecting.
Rogers emerged from the lunch break a different player. Gone was the confidence and timing he had displayed before the interval and in their place were nerviness and uncertainty.
He played and missed several times at Broad and Bresnan before swiping across the line at Swann and getting struck low on the pad in front of leg stump.
At 129-3, England sensed
another Australia collapse,
but Clarke's brilliance and Smith's good fortune ensured the day took a very different course.
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