The third-seeded Bautista Agut denied the second-seeded Pouille his own second title this year and a chance to break into the top-10 rankings for the first time.
Pouille, the winner in Montpellier and runner-up last week in Marseille, looked out of steam in the final. Also, his last three matches were all three-setters.
Bautista Agut came to Dubai on a three-match losing streak after winning in Auckland in January. He was stoic in the final, converting three of his nine break chances, and dropping serve only once.
Of his eight career titles, "It is my best win," he said.
He broke in the fourth game for the first set.
In the second, Pouille led 3-1 but lapsed back into errors and making less than half of his first serves. Bautista Agut broke straight back, and again in the ninth game and served out.
"I didn't give him all the court, all the control of the game," Bautista Agut said. "I was mentally strong. I could come back into the match playing very good tennis (in the second set)."