The home favourite finished his interrupted final round on Monday, shooting an impressive 69 to end four shots clear at 12-under.
The tournament in Andalucia was heavily affected by thunderstorms and had to be completed a day late even after being reduced to 54 holes.
Garcia started the day three ahead with 11 to play, but that lead quickly evaporated as world No. 87 Lowry found three consecutive birdies at the turn.
The 2017 Masters champion, whose own foundation hosts the tournament near Cadiz, then dropped a shot at the 13th to lead by just one.
But he bounced back at the 14th with a fine birdie and was then helped by Lowry’s poor shot into the trees at fifteen which resulted in a costly double bogey.
From there Garcia was in control and although Lowry took the clubhouse lead with a fine round of 66, Garcia cruised home with another birdie at the 17th and a solid par on the final hole.
The victory made Garcia the first player to win the same European Tour title three times in a row since Ernie Els in 2004 when he won a third Heineken Classic in Melbourne.