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)."
Desert Smash: A Celebration of Celebrity, Charity and Tennis Unlike Any Other
The 14th annual Desert Smash charity tennis event is Tuesday, March 6, and there are many reasons to mark your calendar. Here are just five of those reasons, including the event's host, Serena Williams.
Desert Smash is the kick off to Indian Wells, which will be broadcast on Tennis Channel over the next two weeks.
*** STREAM DESERT SMASH LIVE on TENNIS.com ***
*** WATCH LIVE on TENNIS CHANNEL ***
*** PURCHASE TICKETS AT https://desertsmash.