The 22nd-ranked Cilic, playing in his fourth final this season, broke in the sixth game of the first set. Tipsarevic, who won his second career title in Moscow last week, broke early in the second set.
Tipsarevic saved two break points before the fourth-seeded Croat broke him with a precise backhand down the line in the sixth game of the third set.
On his next serve at 5-2 down, Tipsarevic fell to 15-40, but fired an ace and served a winner to save two match points. But on the subsequent deuce, the 13th-ranked Serb returned wide and Cilic converted his third match point with a backhand winner.
"I played the first two sets a little bit up and down and had some unforced errors," Cilic said. "But I played my best tennis in the third set. I lost three finals this year and all of them were in three sets. So today, when the match went into the third set, I was really into it to win."
Tipsarevic took a medical timeout after the first game in the third set to have the back of his right leg massaged and receive treatment for a blister on the little toe of his right foot.
Cilic said he used the time to gather his thoughts.
"As soon as (Tipsarevic) came back on the court to serve, I was ready to push him, push him physically and that was the turning point of the match," he said.
Tipsarevic, who won his first career title in Kuala Lumpur on Sept. 26, said he was tired by the end of the match.
"Marin deserved to win -- he was a better player today," Tipsarevic said. "I really gave everything today, but in the third set I felt it wasn't about tennis; it was about me completely out of fuel on court. I've played a lot of matches in the last two weeks."
Cilic is the second Croat to win the tournament after Mario Ancic in 2006.