The Spaniard took a three shot lead into the final round of the Portugal Masters and birdied the third to keep the chasing pack at bay.
And with no fewer than five players advancing to 16 under par at Oceanico Victoria Golf Course he then hit a three wood approach to the heart of the green on the par five fifth and two putted to reach 20 under for the week.
Martin, the first amateur to taste victory on The European Tour three years ago and winner of the first event on The 2010 Race to Dubai at the Alfred Dunhill Championship, was clear of Richard Green, Peter Lawrie, Jeppe Huldahl and Mikko Ilonen.
Francesco Molinari was also 16 under but already in the clubhouse after his second 62 of the week.
Nine birdies, an eagle and a single bogey in his first 14 holes left the Italian Ryder Cup star in sight of the first 59 in European Tour history but he could only par his last four holes.