Bautista Agut, 30, had lost his past three meetings with Berdych, the 33-year-old former world number four who has slipped to 71 in the rankings.
"Obviously, I'm not pleased that I lost the match today, but I lost to a better player in the end", said Djokovic. Bautista Agut romped through the Swiss in straight sets 6-4 6-4.
"I wasn't the freshest, you know".
The world number one bowed out at the fourth-round stage of the first major of the year 12 months ago after losing in round two in 2017. I'm happy with the way I'm playing.
Ivo Karlovic made history at the Tata Open Maharashtra in Pune by becoming the oldest player since 43-year-old Ken Rosewall at the 1977 Hong Kong Championship to reach a tour-level final.
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.
"I will remember this match all my life", he said after the 3-6 7-6 (8-6) 6-4 win. "He is one of the greatest legends of all time and we want to see him play".
In the second semi-final No. 4 seed Marco Cecchinato from Italy will take on Czech wild card entry Tomas Berdych. The irrepressible Djokovic is set to play his sixth match of the week later on Thursday when he continues his doubles partnership with his brother Marko. With the quality of tennis displayed against Novak Djokovic, Roberto will be the favorite going into the finals.
Agut took Djokovic's serve in the second game of the final set for the decisive break, and secured victory on his first match point. In the seventh game Bautista Agut broke the Serbian but Djokovic wrapped up the set at 6-3.
Things quickly turned in Bautista Agut's favour, though, as his punishing groundstrokes penetrated Djokovic's previously solid defence.