The top-seeded Japanese next faces Pablo Andujar who scored a surprise 7-6 6-3 victory over fellow Spaniard and number three seed David Ferrer.
Nishikori, ranked fifth in the world, was superior to Klizan throughout with his decision-making and execution.
"I am excited to be in the final again. Everything was perfect, the win and also the way I was playing," he told reporters.
"I tried to get a lot of spin on the clay but I also played some flat forehands and backhands so as to mix it up."
Nishikori is breaking new ground for Asian tennis. He is the highest-ranked Asian male in ATP Tour history and is the first to reach a grand slam final, at last year's U.S. Open.
He broke Klizan in his first two service games and while the Japanese began to relax towards the end of the first set he was still comfortably on top.
Klizan held on after a marathon first service game in the second set but Nishikori then eased his way to victory.
Ferrer had looked strong on the other side of the draw but an inspired Andujar hit a series of powerful groundstrokes after a slow start and volleyed well at the net.
World number eight Ferrer broke to go 2-0 up in the first set but his opponent, ranked 66th in the world, battled back to take the set to a tiebreak.
Ferrer fell apart at the start of the second set and Andujar cruised through.
"This is probably the best game I have played in my life as Ferrer is one of the best on clay in the world," he said.
"My game plan was to pressure his second serve and get to the net as much as I could. I played well and he started making mistakes."
(Reporting by Tim Hanlon, editing by Douglas Beattie)
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