The Spaniard started the day one shot behind Anthony Michael but started birdie-eagle to be one in front after just two holes.
South African rookie Michael - who has led after all three rounds so far - managed a birdie of his own at the second, he could only par the next and dropped a shot at the 448 yard third.
Martin then birdied the seventh from nine feet and reached the run in 30 with another gain at the ninth.
Michael pulled one back at the eighth, but a wild tee shot at the 11th led to double bogey and he was five behind with seven to play on nine under.
His compatriot Dawie Van Der Walt was also nine under, but with only six to play it was going to take a remarkable turnaround to catch Martin - who in 2007 became the first amateur winner in European Tour history.