It is the second time Bautista Agut has beaten Djokovic in his career and both victories occurred in a semi-final.
"I will remember this match for [the rest] of my life", said the 30-year-old.
It was only a second win over the Serbian for Bautista Agut - his first coming in 2016 - and it will live long in the Spaniard's memory.
"Under the circumstances I managed to find a way to win against a player that is hitting the ball very fast and just being very aggressive and it's hard to predict where the ball is going to go with a player like him".
Asked about his workload, Djokovic said: 'I wasn't the freshest, you know. Djokovic was also world number 1 at that stage.
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"Roberto was too good, so well done for the title today, but I am happy for the week", the world number 71 added.
Djokovic said that sport needed "legend" Rafael Nadal to make another comeback after it was announced Wednesday that the injury-plagued Spaniard had withdrawn from his season-opening tournament in Brisbane. It ended in a straight-sets defeat.
Later on Thursday, Djokovic spent another 65 minutes on court alongside his brother Marko in a doubles match that they lost in a deciding tie-break to David Goffin and Pierre-Hugues Herbert.
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. Novak was up and it was tough.
The 39-year-old Croat beat Belgian Steve Darcis 7-6 (7) 4-6 6-3 to advance to his first championship match since 's-Hertogenbosch in 2017.
He missed a forehand approach shot and Bautista Agut went on to serve out the match to love. The Serbian has been nearly unbeatable on hard courts over the last six months, but Bautista-Agut trumped him in a tactical masterclass.