The Middlesbrough striker was expected to start the game in Maribor after missing the surprise victory over fellow finalists Serbia last Saturday because he was getting married in England.
"We've had two very competitive games on tour and now it's about protection," Herbert told reporters. "The last thing I want is injuries so we'll be very careful with this group. I'm not interested in the result."
The absence of Killen, who has put his honeymoon on hold until after the World Cup, means Chris Wood of newly-promoted Premier League side West Bromwich Albion keeps his place.
Despite retaining the same starting side that beat Serbia, Herbert said he had not decided upon his preferred line-up for their World Cup opener against Slovakia on June 15 in Rustenburg.
"We've gone for with a bit of stability for this match," Herbert said.
"At the back I think it was important to play Winston Reid and Tommy Smith but there's massive competition there from Ivan Vicelich and Ben Sigmund, and those two will get time either in this match or against Chile."
New Zealand also face holders Italy and Paraguay in Group F at the June 11-July 11 tournament.
