Clarke (109no), already averaging more than 100 runs per innings at his most fruitful venue, batted wonderfully after some early fortune as he and Brad Haddin (57no) took the Australia total from 273 for five to 389 without further loss.
England did not help themselves with some more sleepy and costly work in the field, but nothing went right for them either.
Even when it seemed Ben Stokes had broken the century stand for the sixth wicket, Haddin caught-behind pushing forward, instead Marais Erasmus checked for a no-ball which was confirmed by video replay.
After Haddin therefore retraced his steps back to the middle, there was an ugly reprise of the antagonism which marred the first Test in Brisbane, as batsman and bowler engaged in a verbal confrontation at the end of the over and had to be spoken to by Erasmus.
Clarke was unfazed, and duly reached his second hundred of the series in Stokes' next over - his 26th in all, and seventh in the Ashes - with 11 boundaries from 175 balls.
England had resumed hoping they would not pay a high price for the catches they dropped last night, to reprieve Clarke on 18 and Haddin on five.
Clarke, of course, had the opposite agenda - and it was he who prevailed as Australia, already 1-0 up in this series, piled on England's misery.
The Australia captain was out to impose himself from the outset against Monty Panesar, from the left-arm spinner's first delivery, and squirted two runs just over and wide of cover to complete his 50.
Clarke might easily have gone without addition to his overnight score, after failing to get to the pitch and chancing his arm nonetheless - but thereafter he was masterful.
He targeted Panesar in particular, forcing Alastair Cook to switch to Graeme Swann after four overs which cost 22 runs.
Haddin's first runs of the day took him to 1,000 against England, on his way to the fifth half-century of the innings.
He needed only 71 balls, and hit four fours and two sixes, one of the maximums a streaky one as the ball flew off the upper edge of a slog-sweep at Swann.
Quicker reactions in the field might twice have helped England see off the wicketkeeper-batsman on 18 and then 30.
Michael Carberry was unable to deliver the right throw for a possible run-out after a quick single to short third-man, and then Panesar could not make enough ground to take the catch after a faulty hook at James Anderson.
Clarke had one dicey moment, on 91, when Ian Bell was unable to cling on to an especially tough chance at short-leg as the batsman advanced to Swann and got a thick inside-edge.
For good measure, Clarke also managed to regain his ground before the ball could be ferried back to the stumps by Bell and wicketkeeper Matt Prior.
It was one more near miss which typified a session in which Clarke seized control, and England were unable to resist.
:: Both teams and the crowd observed a minute's silence before start of play, and the players took the field wearing black armbands, in tribute to former South African president Nelson Mandela who died on Thursday.