Isner appeared to be troubled by an arm injury in the Australian Open tuneup event. The American needed treatment on his upper arm or shoulder but still had eight aces and put 78 percent of first serves in play.
Ferrer won the Auckland title in 2007, and Kohlschreiber took the 2008 championship.
"It was another tough match," Ferrer said. "I'm happy in the first tournament of the year to be in the semifinals. It's not easy when you miss two matchpoints but I wasn't afraid. I served well in the late stages of the match, when it was important."