Borrego finished at 7-under 281 in winning his second European Tour title and his first since 1996. Borrego almost lost his tour card in 2001.
Ivo Giner of Spain (73) and Maarten Lafeber of the Netherlands (73) shared second at 282.
As scores ballooned in the gusts, Borrego did not drop a shot after a three-putting for a first-hole bogey.
'I just did fairways, greens and two-putts,' Borrego said. 'When I got to the 12th I told my caddie, 'Now is the moment, now is my good chance to win.'
Giner could have forced a playoff with a par on the 18th but came up short with his 8-iron and missed a 4-foot putt.
'It hurts,' he said.
Roger Winchester of England (67) was fourth at 283 and Charley Hoffman of the United States (71) and Santiago Luna of Spain (70) were at 284.
Full-field scores from the Madeira Island Open