Djokovic had been forced to come from a set down to beat Marton Fucsovics and Nikoloz Basilashvili to earn his previous two victories in Doha, but on this occasion it was Bautista Agut's turn to fight back from behind.
The 30-year-old Spaniard will face Tomas Berdych in the title clash after the Czech beat fourth-seeded Italian Marco Cecchinato 7-6 (6) 6-3 in the other semi-final.
The ASB Classic has lost another top player, with defending champion Roberto Bautista-Agut pulling out of the event due to fatigue. With the quality of tennis displayed against Novak Djokovic, Roberto will be the favorite going into the finals.
Asked about his workload, Djokovic said: 'I wasn't the freshest, you know. The world number one survived a huge scare to eventually triumph 4-6, 6-4, 6-1 Wednesday and admitted his opponent was "very close to the win".
"I can't be more happy than I am right now". That's it, ' a frustrated Djokovic said in his post-match press conference.
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This makes him a risky opponent for Djokovic, although it should be pointed out that their other three meetings on hard courts have all ended in favour of the Serbian.
'What happened? I lost the match. Novak was up and it was really tough. "He has a very physical style of Tennis which obviously is putting a lot of load and pressure on his joints, on his knees". He was solid and I had to play good tennis. "I did everything well today". He hasn't dropped a set this week.
In the decider, the World No. 26 took an early 2-0 lead to put pressure on Djokovic and although the reigning Wimbledon and US Open made a valiant bid to bounce back, Bautista Agut held on to register one of his remarkable wins of his career.
A wide forehand midway through the seventh game gave Djokovic an opening and he duly broke through to love as Bautista Agut found the net with a weak backhand.