Three Toby Flood penalties underpinned a bash-and-smash England display that saw them waste numerous attacking opportunities after enjoying set-piece domination.
Wales, having lost Gavin Henson and Rhys Priestland to first-half injuries, dug deep, conjured a 58th-minute try for full-back James Hook that he also converted, and then comfortably kept England out.
Celebrity centre Henson departed with a wrist problem following an impressive 30-minute display, while fly-half Priestland, who kicked two penalties, hurt his left thigh.
Henson is due to undergo a scan before Wales coach Warren Gatland knows the full extent of his injury. The 29-year-old has never played in a World Cup, with this potential setback arriving just 18 days before departure to New Zealand.
Two long-range Hook penalties then sealed the the deal for a Wales side whose defensive heroics - marshalled by their magnificent captain Sam Warburton - ultimately won the day.
It was just Wales' sixth victory in the last 21 Tests, yet the result should do wonders for morale as they build towards a punishing World Cup pool that also includes South Africa, Samoa and Fiji.
But England will head back to their Surrey training base for a collective bout of head-scratching.
Rarely, in the modern international game, can one team have enjoyed such sustained supremacy but failed to ram home that advantage where it really counts - on the scoreboard.
England's midfield combination of Mike Tindall and Shontayne Hape was again exposed as slow and one-dimensional - Hape's garish green boots were the only eye-catching thing about him - while team discipline creaked far too often.
If the purpose of World Cup warm-up games is to identify problems before the main event, then England boss Martin Johnson will assess the trip to Cardiff as a worthwhile exercise.
But there was nothing in England's display to give any of the southern hemisphere super-powers that await them in New Zealand this autumn the remotest reason for a sleepless night.
Wing Chris Ashton, who scored two tries on England's last visit to Cardiff in February, missed out because of an ankle injury, although his late withdrawal was purely a precautionary measure.
Bath's Matt Banahan replaced him, with Delon Armitage joining the substitutes, while Wales showed four changes from last weekend's 23-19 defeat at Twickenham as Henson, Hook, hooker Lloyd Burns and lock Luke Charteris all started.
Both teams set out their stall by performing at a furious tempo from the start, with Priestland and Flood exchanging early penalties before a second Priestland strike nudged Wales 6-3 ahead.
Much of Wales' front-foot play was created by the offensive work of Henson and his midfield partner Jamie Roberts, who relished the physical nature of their tussle with Tindall and Hape.
Up-front, though, it was a different story as England exerted alarming scrummaging pressure from a Welsh perspective.
A less patient referee than Irishman Alain Rolland would have awarded England a penalty try, but Wales escaped when Henson ankle-tapped Hape and then hoofed the ball downfield.
A second Flood penalty levelled things up and England began to enjoy consistent territorial pressure, eager to put Wales' questionable set-piece through the mill at every opportunity.
Scrum-half Richard Wigglesworth, who had taken a knock, was then replaced by Danny Care, before Henson - who appeared to be holding his arm - made way for Scott Williams nine minutes before the break.
England kept battering away inside the 22, but their lack of craft and guile behind the scrum was exposed, and Wales held out.
Even after Care made a scorching 40-metre break, and then Tindall ran free, England could not finish off, somehow turning quick ball into slow ball, while also continuing to concede penalties.
Johnson cut a frustrated figure from his seat in the stand, and it was difficult not to sympathise with him as England huffed and puffed their way towards half-time after failing to knock down Wales' defensive wall.
Priestland did not reappear for the second period, being replaced by Newport Gwent Dragons wing Aled Brew. Hook moved to fly-half and Shane Williams took on full-back duties.
But before Wales could settle into their new formation, Flood kicked England in front after Roberts was sin-binned for killing the ball.
Rolland was rapidly running out of patience, and Banahan received a ticking-off after further technical indiscipline, although he avoided seeing the yellow card that was brandished at Roberts.
Wales, perhaps not quite believing England's profligacy in attack, rallied well as the third quarter neared its conclusion, and a spell of pressure resulted in Hook claiming a try that he also converted.
For England, there was no way back as, for the first time since the 2010 Six Nations Championship, they failed to score a Test match try.
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