Sousa, who has lost finals in Switzerland, Croatia and Russia in 2015, secured his second career title when he converted four of his five break points to upset seventh-seeded Bautista Agut in front of his home crowd.
The Spaniard, playing his second final in as many weeks having lost to Croat Marin Cilic at the Kremlin Cup in Moscow last weekend, felt the pace as the match wore on and needed treatment after Sousa made it one-set all on the indoor hardcourt.
On Saturday, world number 24 Bautista Agut had battled for more than two hours and had to save six match points to get past American Steve Johnson 4-6 6-3 7-6(8).
Sousa, ranked 46, dropped only one set on the way to the final, his seventh on the ATP Tour, and the Valencia title follows his only other success, in Kuala Lumpur in 2013.
"When he was a break up in the second, I decided to change a bit my tactic and try to be more solid and it was the key," Sousa said.
"I also know he was probably very tired as he had a tough week and, as I said on court, playing at home is great but also adds a bit more pressure," noted the 26-year-old.
"I have been based in Spain since I was 15 years old, so in a way I feel a bit at home and it’s great to be able to win this title here and in front of my family who I had no idea was going to come, they drove 10 hours from Portugal to be here today."
Sousa's victory was somewhat overshadowed by the announcement after the final by tournament director Juan Carlos Ferrero that the event would not be held next year due to a disagreement with the Valencia regional government.
"It’s very sad, of course, so many efforts have been made to promote tennis in this region and have a great tournament here," Bautista Agut said.
"This is a tournament that players like to come and play, for me even more since it's always special to play at home."
(Reporting by Iain Rogers, editing by Ken Ferris)
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