After coming back from a set down against Marton Fucsovics in his second round match, the World No. 1 rallied past Nikoloz Basilashvili of Georgia 4-6, 6-3, 6-4 on Thursday evening to reach the semi-finals at the Khalifa International Tennis and Squash Complex in Doha.
The 30-year-old also has an outstanding record on Stanley Street.
Bautista Agut said Friday's victory was the better of the two.
"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". I know it's hard to play at this level.
The shocking upset over world number one Djokovic comes at a time when the Serbian is red hot.
He added that his immediate aim was to "be fresh" and then win as many matches "as I can" in Melbourne at the Australian Open. Their most recent encounter came at the French Open previous year, when the Serb edged a four-set victory in a Round 32 match. With the momentum swinging his way, Bautista Agut secured an early break in the final set before closing out the match.
He will battle it out with Marco Cecchinato for a place in the final after the Italian made it past Dusan Lajovic 7-6 (2) 6-2.
It was the first time Djokovic has won back-to-back matches from a set down since Cincinnati in August a year ago, a tournament he went on to win. The Serbian player leads head to head meetings 1-0, they already faced each other at the Monte Carlo Masters with Novak prevailing in straight sets, 6-4 6-2.
Things quickly turned in Bautista Agut's favour, though, as his punishing groundstrokes penetrated Djokovic's previously solid defence.