It was Nishikori’s first appearance since the Miami Open semi-final farce – in which Rafa Nadal and Novak Djokovic moved through to the final without hitting a ball after the Japanese number one and Tomas Berdych withdrew.
Despite blitzing his way through the opening set for the loss of a solitary game, Nishikori struggled in the second and was broken three times as the Spaniard drew level.
The pair swapped breaks at the start of the decider before Nishikori gained the upper hand to triumph two minutes shy of the two-hour mark.
"I'm very happy to win," said Nishikori. "I played well in the first and third set and he was more aggressive in the second, I couldn't do anything.
"There was a bit of a momentum shift in the third set. it was a good win for me."
Fifth seed Tommy Roberdo also progressed with a 6-3 6-4 win over Australia’s Marinko Matosevic in front of a home crowd.
Round two results
10-Philipp Kohlschreiber (Germany) beat Edouard Roger-Vasselin (France) 7-6(4) 6-2
Andrey Golubev (Kazakhstan) beat 16-Benoit Paire (France) 6-4 5-1 (Paire retired)
4-Kei Nishikori (Japan) beat Roberto Bautista (Spain) 6-1 4-6 6-3
9-Ernests Gulbis (Latvia) beat Daniel Gimeno-Traver (Spain) 7-5 7-6(1)
Round one results
Round 1 Albert Ramos (Spain) beat Nikolay Davydenko (Russia) 6-4 6-4
Martin Klizan (Slovakia) beat Somdev Devvarman (India) 6-2 6-4
Jurgen Melzer (Austria) beat Mikhail Kukushkin (Kazakhstan) 7-6(5) 3-6 6-3
Ivan Dodig (Croatia) beat Facundo Argueello (Argentina) 6-3 6-7(5) 6-2
- Sports & Recreation
- Novak Djokovic
- Philipp Kohlschreiber