The 29-year-old proved too solid for a listless Nishikori, winning 6-4 7-6(3) 3-6 6-3 on Court Three.
"I could not get into my rhythm," Nishikori told a large gathering of Japanese reporters.
"It was really hard for me to be aggressive today. In the third set I began to move him around a bit but it didn't last long enough unfortunately. I totally lost my rhythm out there."
It has been a mediocre year for Nishikori who is struggling to build on the promise he showed when he reached the 2014 U.S. Open final, losing to Marin Cilic.
After reaching the final in two of his first three tournaments of 2017 he has not made one since and has been suffering with niggling injuries.
On Friday he paid the price for failing to take his break point chances in the first set, especially at 4-4 when Bautista Agut saved one with a crisp forehand winner.
The Spaniard broke in the next game to take the opening set.
It was a similar story in the second set with Nishikori unable to convert any of the five break point chances that came his way before succumbing in a tiebreak in which Bautista Agut reeled off the last four points.
Nishikori, who has never flourished on grass and is yet to go past the fourth round at Wimbledon, did briefly gain the upper hand as he took the third set.
When he broke at the start of the fourth with a running forehand pass, to the delight of his fans, it seemed the match could swing his way but it proved a false dawn.
Eighteenth seed Bautista Agut belted a forehand winner to break back for and delivered another hammer blow to move 5-3 ahead before sealing victory as Nishikori skewed a backhand out.
Bautista Agut will face stiffer opposition on Monday when he plays Croatia's seventh seed Marin Cilic.
(Reporting by Martyn Herman; Editing by Toby Chopra)
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