It's only the second indoor title for the Argentine, who was playing his first event since returning from a right wrist injury that sidelined him for more than a month.
"It's been a fantastic week," the eighth-ranked Del Potro said. "Coming back to the tour and being seeded No. 1 put me under pressure. I am so happy now. Winning a tournament means a lot. It's important to have a good end to the year."
Del Potro improved to 12-5 in finals and is a strong favorite to pick up one of the remaining berths at the season-ending ATP World Tour Finals.
"That was on my mind coming here," he said. "I am looking even better now ... but I still have two big tournaments and must do well in Basel and Paris."
A losing finalist last year, Del Potro survived a shaky start against the 70th-ranked Zemlja, who was the first player from Slovenia to reach a final after upsetting Janko Tipsarevic in the semifinals.
At 2-2 in the opening set, Del Potro lost serve for the first time in the tournament. But from 2-4 down, he won 11 of the next 15 games to close out the victory.
"It wasn't a good start, I was nervous because it was a final," Del Potro said. "In the second set, I broke him early and that gave me confidence to play the final like everyone expected me to do."
Zemlja's defeat left Finland's Jarkko Nieminen as the only qualifier to win an ATP tour event this season, after winning in Sydney.
"I am satisfied," Zemlja said. "My first semifinal, my first final, is was a great week. I am happy with my tennis, I know now that I can beat everybody."
Zemlja started well in the final but only converted one of his five break points to let Del Petro escape. He missed three chances with the Argentine serving at 4-4.
"In the first seven games, I was aggressive," Zemlja said. "I thought I was ahead of him regarding my game plan. It didn't work out in the closing stages of the first set and from then on he was the better player. Del Potro raised his level and his forehand is the best in the world."