slips where Clarke clinched a brilliant catch.
Johnson then bowled paceman James Anderson for another first-ball duck, pegging back his middle-stump for a second attempt at a hat-trick.
Playing a lone hand for England, Ian Bell only just survived the hat-trick ball, his shot falling only a few feet shy of a man at short extra cover.
Bell survived a review for lbw and raised his half-century off the next ball with an elegant cut through point for four, then bashed another two boundaries and a six in the over as number 11 batsman Monty Panesar showed courage under fire to help his partner add 37 for the 10th wicket.
Johnson emerged again to bowl Panesar for two to bring an early tea and leave England reeling.
England paceman James Anderson captured two quick wickets in opener Chris Rogers and Shane Watson but Warner and Clarke steadied the ship with a 61-run partnership.
Clarke was bowled by Panesar for 22 with a delivery that turned sharply to give plenty of encouragement to Australia's spinner Nathan Lyon, and Steven Smith (23 not out) added another 67 with Warner to leave England further demoralised.