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And the top seeds kept falling as women's world number two Petra Kvitova slumped to a surprise 7-6 (8/6), 3-6, 6-2 defeat to Australian Ashleigh Barty.
Bautista Agut, 30, may have beaten Djokovic on the way to winning the title in Doha earlier this year but 15-time Grand Slam champion Djokovic started like a train in this last 16 encounter before being amazingly reined back in.
After just 25 minutes, Djokovic was 5-0 ahead and on cruise control, Bautista Agut severely struggling to keep the Serbian at bay.
A short rain delay late in the second set allowed Bautista Agut to regroup, however.
He returned a completely different player and at the end of an absorbing two hours and 29 minutes, it was the number 22 seed who will now meet defending champion John Isner for a place in the semi-finals.
"I played more aggressive," said Bautista Agut who began to noticeably step inside and force Djokovic onto the back foot. "I tried to miss less balls, to really concentrate on the beginning of the point with my serve, with my return."
With Roger Federer's match with Daniil Medvedev postponed until Wednesday after a spell of heavy rain forced tournament officials into a reshuffle, all the focus remained on Djokovic's shock exit.
The reigning Wimbledon, US Open and Australian Open champion left court and headed straight to a press conference to try and explain this most remarkable of turnarounds at Hard Rock Stadium.
"He is a solid player but I shouldn't have lost this match, I had way too many wasted opportunities," said the world number one, who also failed to make the latter stages of Indian Wells this month.
"I thought I played well today and during this tournament but two or three sluggish games and that's what happens."
Djokovic, who also hinted his vociferous involvement in ATP tennis politics which saw President Chris Kermode ousted this month may have affected his focus, was initially consistent with his serve during the opening set.
He mixed up is shots superbly, blending power and subtlety to keep his opponent guessing.
However, a drop in Djokovic's level coupled with a rise in Bautista Agut's aggression saw a complete reversal in fortunes after a 30 minute weather delay. The Spaniard grabbed two set points, the second of which was taken when the Serbian netted a forehand.
Bautista Agut broke again for 3-1 in the third following an uncharacteristic double fault and although Djokovic hit back in the very next game, the Spaniard again took advantage of his opponent's faltering serve to move within two games of victory.
Serving for the match, he brought up two match points, another forehand winner sealing one of the best comebacks of his career and his third win over the world number one from their last five matches.
Big-serving Isner moved into the last eight with a 7-6 (7/5), 7-6 (7/3) triumph over Great Britain's world number 22 Kyle Edmund.
Elsewhere there was a brilliant win for 18 year-old Felix Auger-Aliassime, the Canadian who came through qualifying, who beat Georgia's Nikoloz Basilashvili 7-6 (7-4), 6-4.
Auger-Aliassime, who is set to become the first player born in the 2000s to break into the top 50 when the rankings are updated next week, plays Borna Coric after the Croatian beat Nick Kyrgios 4-6, 6-3, 6-2.
The controversial Australian was furious after being heckled by a fan during the third set and was docked a point after responding with an expletive. Something similar happened Sunday night.
"I'm not going to take it," said Kyrgios, who admitted he became "a little bored" during the second set."
In the women's draw, Barty, who beat Kvitova for the first time having gone into the clash 0-4, will play Anett Kontaveit for a place in Saturday's final after the Estonian brought an end to Hsieh Su-Wei's impressive run with a 3-6, 6-2, 7-5 victory to reach the last four in South Florida for the first time.
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