It was the ninth career title for the top-seeded Japanese, who again showed his improved endurance as he battled to come out on top against the world number 66.
"I didn't think about winning the tournament at the start of the week because of the strength of the players here, especially the Spanish, but now I am very happy," Nishikori told reporters.
"I knew that Andujar has a good backhand and my plan was to move the ball around a bit. It worked well in the last few games and then with the final shot I closed my eyes and it went in."
Andujar broke serve in the opening game with Nishikori making uncharacteristic mistakes and the score was 2-2 before either player held serve.
Nishikori found himself being dragged out of position by Andujar, who had beaten third seed David Ferrer in the semi-finals but, despite racking up 13 unforced errors, he still managed to break his opponent again at 5-4 to win the first set.
Nishikori continued to make mistakes as the Spaniard went into a 2-0 lead in the next and then survived a break point to go 3-1 ahead.
Yet the Japanese world number five rallied to level at 4-4 before, in Andujar's next service game, a double fault gifted Nishikori match point and a backhand down the line gave him victory.
Nishikori exploded on the tennis scene last year, reaching his first ever Grand Slam final at the US Open and he will be among the favourites to win the French Open next month.
Strong from the back of the court, he is well suited to clay courts, also having reached the final of the Madrid Open in 2014 where he had to retire injured against Rafael Nadal.
(Editing by Ian Chadband)
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