He was at 8-under 205 entering Sundays final round, the only golfer under par in each round. Goya, who won the Tour de Las Americas Order of Merit last year, bogeyed the fourth hole but came back with birdies at the fifth and sixth. He also birdied the 11th and the 14th but bogeyed the 13th.
Goyas closest pursuer was Irelands Damien McGrane, who shot a 70 despite two bogeys in the opening five holes. Spains Carlos Rodiles was a shot behind in third after a 71.
The Seve Ballesteros-designed Porto Santo course is on a small island off Madeira, a Portuguese archipelago in the Atlantic about 400 miles west of Morocco.
Second-round leader Michael Hoey of Northern Ireland dropped to fourth after a 75. Hoey had a 66 Friday but dropped three shots on the opening three holes and had a double-bogey at the 10th.
Scotlands Callum Macaulay recorded the days best score of 67, which included one eagle and four birdies. He was 2 over and shares 10th place.