Bautista Agut will rise one place in the world rankings to 23 on the back of the victory in Qatar, and said his aim was to go higher.
The World Number one was imperious in the first set and looked composed through breaking his opponent in the second game and holding his serve to take a commanding 3-0 lead.
Bautista-Agut's first round match was scheduled for Tuesday, which would have given him little time to acclimatize, and also recover from the long 17-hour journey from the Middle East.
The world number 24 triumphed in one hour 55 minutes in Doha to claim his ninth ATP Tour title.
"I will remember this match for [the rest] of my life", he said after the match.
"I can´t be more happy than I am now".
Berdych raised his level in set number two, serving well and scoring a break in the fourth game thanks to a volley victor, jumping into a lead and keeping it throughout the set with three good holds.
Spain's Roberto Bautista Agut celebrates with the trophy after winning the final against Czech Republic's Tomas Berdych. I missed some easy balls and that's what you get as a result of losing the focus in the most important moments and it happens, it happens'.
Victory capped a career week for Bautista Agut, who beat three players who have reached the top five; Stan Wawrinka, Djokovic, and Berdych.
"I wasn't the freshest, you know. Obviously very, very pleased to have gone one step further than a year ago". Still, Djokovic endured and eventually won the twelfth game after nine minutes to set up the tie-break.
Berdych eased through to his second Doha final in straight sets, beating Italy's Marco Cecchinato 7-6 (8/6) 6-3.