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from a groin injury and his withdrawal is another big loss for New Zealand's pace attack after Tim Southee was withdrawn on Thursday with a minor hamstring strain.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."
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)
