It ended in a straight-sets defeat.
In total, Bautista Agut only lost two sets all week in his five matches.
If he wins his last eight match, Djokovic is on course to meet Stan Wawrinka in the semifinals after the Swiss also won Wednesday, beating Chile's Nicolas Jarry 6-4, 7-6 (7-3).
"Long matches today, both singles and doubles, and I spent quite a bit of time on the court but I'm happy I managed to get two wins", said Djokovic. "It was an unbelievable atmosphere", Bautista Agut, 30, said after the pulsating clash. I know it's hard to play at this level.
Novak Djokovic had to work again in Doha. So many times I found myself in defense.
"I wanted to give everything I had in the match and fight until the last point", Bautista Agut added. Novak was up and it was really tough.
"He's definitely one of the greatest hitters in the game and I wish him all the best for the rest of the season". "Today I was very consistent and played with a lot of rhythm".
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.
The first set was like a walk in the park for the World No.1 as his all-around game proved too solid for the seventh seed, with Djokovic winning it at 6-3.
At the Maharashtra Open in Pune, Steve Darcis became the first unranked player to reach a semi-final in the ATP Tour's history. He hasn't dropped a set this week.
Bautista-Agut is in some of the best form of his life, demonstrated by his stunning three set victory over Novak Djokovic last week in Doha.
The Spaniard made the decisive break of serve in the third game of the final set to take a lead he never lost. "In conditions like this, it's quite suitable to him", Djokovic said of Bautista Agut.