The 23 year old Englishman, looking for a first European Tour title after a string of near misses, had started the day well clear of Clarke and Shane Lowry, but bogeyed the par three second.
Northern Irish veteran Clarke, on the other hand, birdied the third to move within striking distance on six under par.
Lowry, partnering Wood in the final group, dropped three shots in his first two holes as his challenge faltered.
England's David Lynn birdied the first to join Ryder Cup Captain José Maria Olazábal in third place on four under par, still four behind Wood.
Wood dropped another shot at the third but a birdie at the fourth relieved the pressure.
Having turned in a one over 36, Wood was suddenly four in front again when Clarke double bogeyed the 11th after finding water.
The Ryder Cup Vice Captain was back into a tie for second with Lowry – who fought back into contention with four birdies in five holes around the turn only to, like Clarke, double bogey the 11th – and Scot Alastair Forsyth, who was two under for the day with three to go.
Clarke saved par well from eight feet at the 13th, and the 12-time European Tour winner was suddenly within two again as Wood three-putted the 12th and 13th to fall back to six under.
The drama was really building as Clarke – whose last victory came at the 2008 KLM Open – holed his birdie putt from off the green at the 14th.
Clarke hit his approach to six feet at the 15th, and knocked in the birdie putt to draw level with three to play.
Wood’s misery continued as he drove out of bounds at the 15th and he had to go back to the tee.
Clarke was having no such problems – he found a bunker from the tee at the 16th but still managed to find the heart of the green with his approach – although he couldn’t hole a third consecutive birdie putt.
Wood kept the drama alive when from behind the green in four, he chipped in to limit the damage to a bogey, and keep him only one behind with two to play.
Clarke pushed his approach right at the penultimate hole and left himself a near-impossible flop shot from behind a bunker, which he did well to keep on the fringe of the green.
Remarkably he chipped in to save his par, and with Wood duffing his chip to the 16th and bogeying the popular Northern Irishman was two clear.