Nishikori fended off the only break point he faced, and broke Matosevic five times.
The U.S. Open finalist will play Jarkko Nieminen of Finland for the first time for a place in the final.
Nieminen took out Pablo Andujar of Spain 6-3, 6-4 to reach his second semifinal of the year.
In Gulbis' way will be fourth-seeded Julien Benneteau of France, who beat fifth-seeded Pablo Cuevas of Uruguay 6-3, 6-7 (3), 6-4 to have a shot at making the final for a third straight year. He has yet to win an ATP singles title.
He broke Cuevas four times, and took 2 hours, 19 minutes to prevail at Putra Stadium.