Two brilliant free kicks from Slovenian star Milivoje Novakovic - one following an awful refereeing decision -- and a third goal from an error by New Zealand goalkeeper Mark Paston on the stroke of halftime saw the hosts maintain their imposing home record.
Rory Fallon scored New Zealand's only goal in the 20th minute but they created several other clear chances in some encouraging signs before their arrival in South Africa tomorrow.
The Ryan Nelsen-led defensive line was again solid as they denied the hosts, ranked 25th in the world, in a goal-less second half.
Herbert praised the performance of young defenders Winston Reid and Tommy Smith whose performances today and in last week's 1-0 defeat of Serbia may have put veterans Ben Sigmund and Ivan Vicelich under severe pressure to make the starting 11 in the World Cup.
"Both are certainly putting themselves in the shop window for us," Herbert said after the match.
Most disappointing was the All Whites' inability to make more of the scoring chances they created.
"It was a frustrating game, a stop start affair, but I think we created hell of a lot of chances which was great but on any other day we could have scored four," Herbert said.
New Zealand, playing without striker Chris Killen who was ruled out with a calf strain were a goal down in just the seventh minute when Nelsen conceded a marginal free kick as he challenged in the air just outside the penalty area.
Novakovic curled a pinpoint effort over the New Zealand wall and Paston had no chance to his right.
New Zealand fought back after a sluggish start but Chris Wood missed two clear chances created by Simon Elliott and Leo Bertos.
They were finally rewarded on the 20-minute when Jeremy Christie sent a long ball in, Wood nodded down and Fallon slammed a left foot volley to goalkeeper Samir Handanovic's left.
There was controversy as Slovenia reclaimed the lead through a refereeing blunder which left the New Zealanders fuming.
Novakovic dived theatrically as Reid contested the ball and clearly made no contact, but the referee was convinced and Reid was yellow carded to add further pain.
Novakovic went low and to the right of the wall with his free kick and Paston again had no chance.
New Zealand had their chances to draw level again before the break, but Handanovic got his fingertips to shots by Shane Smeltz and Wood.
The killer blow came just a minute before halftime when Paston blundered on a regulation save and Andraz Kirm tapped in from close range.
Paston had joined the pre-World Cup chorus of concern about the new ball being used and its quirky flight may have caused some issues.
Herbert made just one halftime change - striker Jeremy Brockie for Wood - although his arrival was far from simple.
Sideline officials questioned Brockie's playing number and he wasn't allowed to enter the pitch before he switched to Aaron Clapham's No 16 shirt.
A baffled Nelsen was also forced to depart and change shirts after the referee objected to him arriving without a number on his back after halftime.
New Zealand competed strongly in the second half but couldn't crack the Slovenians. Their best chance of the half fell to Reid who was unmarked from an Elliott freekick but headed over the bar.
Herbert said the pleasing thing was the All Whites' ability to adapt to a tactical change in the second half and keep their opponents scoreless.
". . . we'll be ready come Slovakia (on June 16 NZt)," Herbert said.
"We are `batting' way up above our weight now . . . and if anybody wants to take us lightly at the World Cup, then good luck to them.
"We have shown we have got some strengths that are causing these teams problems."
The All Whites will play one more warm-up match against Chile (Thursday morning NZt).
