The 30-year-old also has an outstanding record on Stanley Street.
Djokovic's first-set problems from earlier in the week were quickly forgotten as he raced into a 3-0 lead, the top seed breaking at the first attempt as a Bautista Agut backhand drifted wide.
"Obviously, I'm not pleased that I lost the match today, but I lost to a better player in the end and I have to turn the next page".
Another day, another struggle for Novak Djokovic.
"Roberto was too good, so well done for the title today, but I am happy for the week", the world number 71 added. Their most recent encounter came at the French Open a year ago, when the Serb edged a four-set victory in a Round 32 match.More news: President Trump makes surprise appearance in White House briefing room
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At the Khalifa Tennis and Squash Complex, Bautista Agut, ranked 24 on the ATP computer, outplayed the two-time Doha champion in two hours and 35 minutes.
The Italian player took advantage of Guido Pella's retirement on Wednesday, Cecchinato is coming from the best season in his career.
The first win came in October 2016 at the Shanghai Masters when Djokovic was also No 1 at that stage.
Berdych - playing in his first tournament in six months after a back injury - saved three set points before moving ahead, the Czech converting his fourth match point to complete a 7-6 (8-6) 6-3 victory.
After securing his semi-final berth, the irrepressible Djokovic then headed back out to court to play his sixth match of the week in the doubles with his brother Marko. However, Djokovic's fortunes changed in the second set when he broke the Georgian in the fifth game and slowly took control of the match.
Djokovic and Nadal have met in the finals of all four of the Grand Slams and 52 times in total.