The Spanish veteran, a former top 10 player now down at 60 in the world, edged out his 33rd-ranked rival from the Czech Republic 7-5, 6-1.
Bautista-Agut had seen off Lehecka in the Davis Cup in September before the Czech gained revenge with a second-round win at the Beijing tournament.
"This one is very special," said Bautista Agut whose last title had come in 2022 at Kitzbuehel.
"I broke my foot last year and I had to fight so hard this year. I went back to 120 in the world, but I was still going to practice with a smile on my face, trying to be a better player, to fight until the end of my career.
"I think I deserved a week like this."
Bautista Agut is the second oldest men's champion on the tour in 2024 after 37-year-old Novak Djokovic claimed Olympic gold in Paris in August.