Clarke went around in 1-under 69 to finish with a 6-under overall score of 274.
Wood held a comfortable margin over Clarke and Shane Lowry (74) going into Sunday’s final round at the Pula golf course, but a disastrous back nine cost the English player his maiden European Tour victory.
Clarke narrowed Wood’s advantage to just one after three holes before a double bogey 6 at the 11th provided Wood – who was 1-over over the front nine – some breathing space.
But the 23-year-old Wood three-putted at the 12th and 13th before powering his drive out of bounds at No. 15, where Clarke’s birdie 3 put him one ahead and in the lead for good.
Wood’s back nine 40 left sent him to a 6-over 76 that left him tied with runner-up David Lynn (70) of England.
“It was an extremely tough day on the course and it was a bit of a grind all the way round,” Wood said. “When you start dropping shots and you hit one out of bounds your head starts going all over the place and it’s difficult to keep going really.”
The 42-year-old Clarke takes home a ?166,660 ($235,000) paycheck with his 13th career European win and first since 2008.
“It’s a bit of a monkey to get off my back after three years not winning so it’s good,” Clarke said. “At the same time I feel a lot for Chris Wood – he’s a young guy, a great player and I’ve been in his position before.”
Alastair Forsyth (70) finished four shots back in third, one better than Paul Lawrie (70) of Scotland, Irish player Shane Lowry (74), Graeme Storm (70) of England and Spanish golfer Jose Maria Olazabal (73), who helped redesigned the course where he won in 2005.