Boult failed to recover sufficiently from a groin injury and his withdrawal is another big loss for New Zealand's pace attack after Tim Southee was withdrawn on Thursday with a minor hamstring strain.
"Trent did everything possible to get himself ready for this test and is extremely disappointed to be missing out," New Zealand selector Gavin Larsen said in a statement.
"While he has made good progress, after training yesterday we spoke with medical staff and it was agreed that Trent required a little further time to be ready for the demands of test cricket.
"Scott will come in as cover having consistently finished as one of the top wicket-takers in the Plunket Shield in recent seasons."
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Kuggeleijn had initially made himself unavailable for selection this season as he was embroiled in a court case over an alleged rape. He was found not guilty last month after a trial in Hamilton.
The third test starts at Seddon Park in Hamilton on Saturday. The Proteas hold a 1-0 lead in the three-match series after an eight-wicket win in the second game in Wellington.
(Reporting by Greg Stutchbury; Editing by Nick Mulvenney)
