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Cruden, a late substitute for Dan Carter who withdrew on Friday with a leg injury, kicked four penalties and three conversions to leave the Millennium stadium with a 100 percent record.
The win extended the All Blacks' unbeaten record to 20 while Wales, who completed a third Six Nations grand slam in seven years last March, have now lost their last six games in a row.
Saturday's match was effectively over at halftime when the All Blacks led 23-0 although Wales, after slumping to defeats by Argentina and Samoa in their opening two November tests, at least showed some fight in the second half with two tries to New Zealand's one.
Flyhalf Rhys Priestland, one of several Welsh players who have failed to recapture the form they showed at the last Six Nations championship, tested the New Zealand defence against the high ball with his first kick of the game, hoisting a punt which left wing Julian Savea spilled forward.
From the resulting scrum Wales won a penalty within kickable distance but surprisingly decided to kick for touch. New Zealand cleared and Wales spurned another penalty within range which Priestland unforgivably wasted by kicking the ball dead.
The All Blacks regrouped, surged into Welsh territory and Cruden kicked his first penalty of the match in the ninth minute. Two more equally composed efforts followed in the next 15 minutes to put New Zealand 9-0 ahead.
Messam's try in the 25th came from a couple of sublime touches by Savea, who more than atoned for his early mistake.
Savea leaped high in an attempt to grasp another Priestland up-and-under and tipped the ball back to Israel Dagg.
The fullback cut through the Welsh defence and hurled a low, fast pass back to Savea who stooped to snap up the ball safely and hurtled towards the corner.
When the move broke down the ball was quickly recycled right with Messam in the clear to saunter over the line.
A promising move by the Welsh, with centre Jonathan Davies combining with left wing Liam Williams to scythe through the All Blacks' defence, came to nothing.
Prop Paul James knocked on the simplest of catches but Wales had already won a penalty which Priestland promptly squandered by kicking the ball dead for a second time.
On the stroke of halftime, New Zealand scored a second well-constructed try with a replica of the move which gave them their only try of last year's World Cup final.
Sam Whitelock soared high in the lineout and prop Tony Woodcock, as he had in the one-point win over the French at Auckland's Eden Park, thundered through a gap to score.
New Zealand went straight back on the attack in the second half with Cruden kicking his fourth penalty in the 41st and lock Luke Romano scoring his first international try seven minutes later when he powered through an attempted tackle by right wing Alex Cuthbert.
Wales gave their supporters something to cheer at last when they won their lineout on the New Zealand line and the entire Welsh XV joined the shove which sent replacement centre Scott Williams over the line for a try. Cuthbert scored a second four minutes from time in the right hand corner.
Williams had taken over from the injured Jamie Roberts in a bleak period for the Welsh in the first half during which they also lost lock Bradley Davies and prop Aaron Jarvis, who was taken off on a stretcher, to injuries.
Davies had collapsed on the ground after a stiff arm tackle to the neck from All Blacks' hooker Andrew Hore in the opening exchanges which incensed the crowd but appeared to go unnoticed by South African referee Craig Joubert or his assistants.
Joubert did, though, send Corey Jane to the sin-bin for a deliberate knock-on by the New Zealand right wing midway through the second half.