Defending champion Murray knocked out home favourite Rafael Nadal in the other semi-final at the Caja Magica, repeating his victory over the Spaniard in last year’s final as he won 7-5 6-4.
Djokovic looked on course for a comfortable win after breaking world number six Nishikori twice in the first set and earning three match points in the second when he was 5-4 up.
The Japanese fought back, saving the three match points and breaking the Serb before forcing the tie break where Djokovic prevailed 7-4.
The 11-times grand slam winner beat Murray in straight sets in the Australian Open final in January and Djokovic is excited to be renewing his rivalry with the Scot.
“Andy has improved tremendously on clay and has proved he is definitely one of the best in the world on this surface,” he said.
“The rivalry continues and we’ve had so many good finals. I look forward to another one.”
Earlier, Murray broke Nadal in the Spaniard’s second service
game but lost his serve before breaking his opponent again to clinch the first set.
LOTS OF PRESSURE
The Scot broke Nadal’s third service game in the second and held his serve, taking advantage of a second match point after spurning the first.
“It’s easy after winning a tight first set to drop your intensity or your level and I really tried to stay on top at the beginning of the second and that was important,” Murray said.
“Rafa doesn’t serve as hard as everyone else but he puts a lot of pressure on your return because if you don’t hit a good one he dictates the point straight away with the forehand. I was able to get some quite good direction on the returns and I think that helped me a lot today.”
Nadal said Murray deserved to win but added that the defeat, which prevents the Spaniard from collecting a third successive ATP title after winning the Monte Carlo Masters and the Barcelona Open, would not affect his mentality ahead of the French Open later this month.
“I played aggressively and to win but he served really well,” said Nadal.
“In general he was a little better than me and I congratulate him for the victory because he was more effective in the crucial points.”