Djokovic claimed he “should not have lost” the match against Agut and believed he suffered from too many “sluggish” games.
The world No 1 also felt he wasted too many opportunities over the course of the match as he was beaten 1-6, 7-5, 6-3.
Djokovic, who is a six-time champion in Miami, got off to a strong start in the match but struggled to dominate the tie after a 30-minute rain delay near the end of the second set.
The Serbian praised Bautista Agut for coming back in their match but felt he still should have been the one to the progress to the fourth round.
“He’s solid player. Congratulations to him definitely for a great comeback,” Djokovic said.
“But this kind of match I should not have lost. So many opportunities.
“Just way too many wasted opportunities.
“This is what happens when you don’t capitalise on time.”
After the delay Bautista Agut came out stronger and saved six of seven break points to take the match into a deciding set.
Djokovic’s loss in Miami was the first he has ever suffered in Florida after he had won the first set – he had a 41-0 record going into the match.
“I don’t know. I mean, I thought I played well today and throughout this entire tournament,” Djokovic added.
“I just — yeah. One, two, three sluggish games, and that’s what happened.”
Although the result was a surprise this wasn’t the first time Bautista Agut had beaten Djokovic.
During the Qatar Open in January he beat Djokovic 3-6, 7-6, 6-4.
The Spaniard, who will now progress to the fourth round, felt his attacking approach was key to finding the victory.
“I played more aggressive,” Bautista Agut said.
“I tried to miss fewer balls, to be really concentrated on the beginning of the point with my serve, with my return.
“At the end, it worked well.”