Matt Henry was expected to be elevated to share the new ball in Hamilton with Tim Southee, although New Zealand delayed naming their side until Friday's toss.
New Zealand coach Mike Hesson said Boult had been troubled by "minor discomfort" in his left knee since the recent India tour and irritated it further in the first Test against Pakistan which New Zealand won by eight wickets.
"We were optimistic he would be ready for Hamilton, but during training on Wednesday he felt further pain and has subsequently been ruled out of the Test," Hesson said.
With the Seddon Park wicket expected to produce more swing that Hagley Oval did for the first Test in Christchurch, Doug Bracewell has been added to the New Zealand squad.
Pakistan, who have not lost a series to New Zealand for 31 years, have fond memories of their last appearance in Hamilton nearly six years ago.
They beat New Zealand by 10 wickets and Asad Shafiq, who scored 83 in his sole innings then, said they need to repeat that "aggressive" approach.
"I remember that innings. I played good positive cricket and it really feels good to come back to the same ground," he said Thursday.
"It seems a bit bowler-friendly wicket, some grass on it, but ... we're used to playing on these wickets in our domestic cricket.
"It's a good challenge for us. We have to play positive and we have to play aggressive on this wicket."
Senior New Zealand batsman Ross Taylor, who had innings of six and eight in the January 2011 encounter, confirmed he will undergo surgery next Wednesday, immediately after the Test, to remove a growth in his left eye.
The 77-Test veteran, who was confirmed to play Wednesday after consulting an eye specialist, has been in poor form, amassing only 103 runs in his past 10 innings.
Taylor said although the growth did not affect his sight it was distracting mentally "when you play and miss the first couple of balls".
After consulting a range of optometrists and specialists, he was confident an operation would clear up the issue.
"In any operation there's a chance things won't go as well as possible but the surgeon I talked to last night was pretty confident," he said.
Taylor revealed the growth had been present for more than five years but had worsened in the past year.
"In all the Tests I still had very good vision, It's just I guess the growth has come across," he said. "The only thing you can really do is wear sunglasses and put eyedrops in."