Nishikori, the 16th seed at next week's Australian Open, turned the tables on the rangy Czech after an earlier loss to take the title 6-4, 7-5.
He was watched in the stands by former French Open champion Chang, a three-time winner at the Melbourne venue in 1995-97.
It continues a promising start to the year for the 24-year-old who was eliminated in the Brisbane International semi-finals by Lleyton Hewitt.
Nishikori broke Berdych in the second game of the match to steam to a 3-0 lead. He served for the set at 5-3 but was broken.
Berdych got to 40-15 and looked like he was going to square the set at 5-5 but the Japanese No. 1 fought back to take it out.
The match appeared headed into a third set but Nishikori saved two break points at 5-5 and then broke the Czech to wrap up the title with a searing cross-court backhand.