Boult's withdrawal comes less than 24 hours after that of fellow bowling ace Tim Southee with a hamstring injury and severely tests New Zealand's pace bowling stocks, as they attempt to salvage a series draw against South Africa.
Larsen hinted that Neil Wagner and Matt Henry were likely to lead the attack in the absence of Boult and Southee.
"Not having Trent or Tim available fests the depth of our squad, but we're confident of the job that Neil and Matt can do for us.
Kuggeleijn, who has not previously played for the Black Caps, but has represented New Zealand A, was accused of raping a woman in her bed in May 2015.
But after a two-year battle to clear his name, Kuggeleijn, 25, received the "not guilty" verdict on February 24, with the jury spending less than an hour in deliberation.
With the court case hanging over his head, he had continued to play for Northern Districts this summer.
In 51 first-class matches, he has scored three centuries with an average of 30.98 runs, while taking 166 wickets with a best of 6-60.
"One thing I will say, I've been incredibly impressed with Scott and the way he has handled himself, on and off the park, with all that's gone on," Larsen told Radio Sport's Martin Devlin.
"He's a resilient man and, [if selected] I think he'll do the job and will be focused."
