The 37-year-old Briton, competing on a sponsor's invite after being forced to go to Qualifying School last year, took the first prize of 750,000 euros ($937,800) after a closing five-under-par 66 earned him a six-under tally of 278.
Swede Fredrik Andersson Hed (67) was joint second on 279 with Briton Luke Donald (71), who saw his victory hopes go up in smoke with a double-bogey seven at the long 17th.
Stephen Gallacher of Britain carded a 70 to finish fourth on 280.
"It's been a long time since I've been in contention, let alone at a tournament like this," Englishman Khan told reporters after claiming his second tour victory, almost six years after his first at the 2004 Wales Open.
"This event seems to bring the best out of me and I drew on some good experiences from the past. I've been struggling with my putting all week but I managed to hole a few today."
