The Spaniard trailed by a shot from Anthony Michael heading into the final round, but his two-under-par 70 enabled him to end on 11 under overall. South African Michael's 73 meant Martin won by two shots at the Leopard Creek Country Club.
But the win did not come without drama, with nerves seemingly getting the better of both men towards the end. Malaga golfer Martin, who had a five-shot lead with six holes to play, saw that advantage quickly eroded as a bogey on the 14th and triple bogey on the 17th meant there was only one shot in it heading into the last.
But Martin birdied the par-5 18, while his rookie playing partner could only manage a par after finding the water when he had little option but go for the green.
Michael finished tied for second, alongside Denmark's Thorbjorn Olesen, who carded a round-of-the-day 66, and countryman Charl Schwartzel, who posted a 70. Another South African, Thomas Aiken, turned in a good showing to sit a shot back in fifth place after ending with a 70 for a seven-under total of 281.
Robert Dinwiddie was the highest-placed Briton after his two-under-par 70 enabled him to finish a shot further back.
Dinwiddie's fellow Englishman Robert Rock - a player who finished fourth and second in the two previous years - completed the co-sanctioned European and Sunshine Tour event in joint-eighth place this time following a 71, with Scotland's David Drysdale coming in alongside him after carding the same score.
The day, though, was a special one for Martin after beginning it a shot behind Michael. He started with a bang after picking up a birdie and eagle in his first two holes and made the turn in a supreme 30.
Michael, the overnight leader for all three rounds, then suffered even further with a double bogey on the 11th as the lead was stretched to five shots. "I played really well on the front nine, I didn't get myself into too much of trouble and rolled out a few good putts," Martin said after clinching his third European Tour title.
"So it was really nice to have that sort of good start and have a bit of a cushion, which in the end I needed." Martin becomes the first golfer in two years to retain a title on the European Tour - with the last man being Ireland's Padraig Harrington after he won The Open at Carnoustie in 2007 and at Royal Birkdale in 2008. Drysdale got his season off to a satisfactory start after picking up a cheque for just over 19,000. He finished four shots ahead of fellow Scot Alan McLean (68) but Scott Jamieson dropped down to a tie for 30th following a closing 77.