The third-seeded Frenchman, a U.S. Open quarterfinalist earlier this month, clipped a neat volley for match point and then hit an ace down the middle.
The 22-year-old Pouille tilted his head back and then wagged a finger in celebration, before the 10th-ranked Thiem hugged him at the net.
''I'm really happy to win my first title here. I played well from the beginning,'' Pouille said. ''Now I can rest and get ready for (the China Open) next week in Beijing.''
It has been a breakthrough year for the No. 18-ranked Pouille, who has beaten five top 10-ranked players this year - including Rafael Nadal at the U.S. Open.
''Since beating (David) Ferrer in Miami, there hasn't really been a moment where my level dropped,'' Pouille said. ''I can't stop now; the tennis road is very long.''
Pouille gave special thanks to his coach, Emmanuel Planque, who looked tearful when Pouille made his victory speech.
''Thanks Manu, for everything,'' Pouille said. ''It's in large part thanks to you that I'm here now.''
Pouille won 83 percent of points on his first serve and saved the only break point he faced in the first set.
Thiem, who was bidding for his eighth career title, saved all three break points in the first set, but Pouille broke him twice in the second.
''It was a very good first set from both of us, not many chances to break,'' the 23-year-old Thiem said. ''I was 4-0 up in the tiebreak but Lucas was the better player and deserves his first title.''
Thiem, a French Open semifinalist this year, is in contention to qualify for the season-ending ATP Finals for the first time. He is in seventh position in the race for the ATP Finals to be played in London in November, with five of the eight slots still up for grabs.
''It's a long season, but I was feeling well (today),'' he told French television. ''I'm happy with how I played.''