But a century partnership between Young and Devon Conway restored the dominance of bat over ball that has been evident throughout the match before a rash shot gave England hope.
Conway top-edged an attempted sweep off Jack Leach which was well taken by Jonny Baristow at deep square leg to bring Henry Nicholls to the crease before Tea.
Joe Root and Ollie Pope had both made the most of the favourable batting surface to make centuries on Sunday but Root fell short of a double century.
Root, on 163 overnight, looked in positive mood and his audacious, Twenty20 style scoop off Tim Southee indicated he wanted to progress at haste.
But Root had added just 13 runs when he drove Boult to Southee at extra-cover and New Zealand wasted no time in exposing England's tail.
Stuart Broad's edge off spinner Michael Bracewell was superbly caught one-handed by Daryl Mitchell and Ben Foakes's useful innings ended on 56 after he was run-out following a mix-up with Matthew Potts.
Potts was bowled by a lovely inswinger from Boult and Bracewell picked up his third wicket to end England's innings with Anderson stumped and New Zealand 14 runs ahead.
Boult ended with figures of 5-106, the 10th five wicket haul of his test career and the fifth time he has reached that mark against England.