Wales were awful in defeat to Argentina last weekend, and there was no improvement against the South Sea Islanders from the Six Nations champions, who face world champions New Zealand next.
Leigh Halfpenny kicked four penalties and converted Ashley Beck's first-half interception score, but it was not enough as Samoa gained revenge for their World Cup reverse of 13 months ago.
The writing had been on the wall when Fa'atoina Autagavaia crossed for the visitors after just 64 seconds, with second-half tries from George Pisi and Johnny Leota sealing the win and Tusi Pisi kicking 11 points.
Wales were without Adam Jones, Dan Lydiate, Alun Wyn Jones, Matthew Rees, Josh Turnbull, Rob McCusker and Jonathan Davies, and they picked up further injuries to hooker Richard Hibbard, fly-half Dan Biggar (both shoulder) and lock Ian Evans (knee).
The manner of the injuries suffered by Hibbard and Biggar may yet occupy the attention of citing commissioner Paul Minto.
Hibbard was felled by a crunching tackle from the outstanding Taiasina Tu'ifua, in which the Newcastle number eight did not appear to use his arms, and eventually forced off to have his arm put in a sling.
Biggar, meanwhile, was on the end of a reckless challenge from Teofilo Paulo, in which the lock led with his head.
Hibbard's replacement Ken Owens was also dragged to ground by the neck by Maurie Fa'asavalu.
Interim head coach Rob Howley said: "Dan and Richard have taken blows to their shoulders.
"It is not the time to discuss anything, but I don't think they were legal tackles as far as we are concerned having looked at the footage.
"It is disappointing to lose players. Dan and Richard had been given an opportunity and Ian Evans has hurt his knee. But it might give someone else an opportunity next week and will test our strength in depth."
Wales are currently unrecognisable from the side that reached the World Cup semi-finals 13 months ago.
But Howley, who hands the reins back to British & Irish Lions coach Warren Gatland for games against the All Blacks and Australia, rejected suggestions from the Samoan camp that Wales' game plan has become easy to predict.
He said: "We have changed since the Australian tour. If they are saying that, it's up to them, but we have a belief in the way we want to play.
"We want strong runners and to put sides under pressure with our kicking game.
"But international rugby is about accuracy and we weren't accurate enough."
Victory puts Samoa in with a real chance of securing a top-eight place in the IRB world rankings ahead of December's 2015 World Cup draw, and leaves Wales in danger of dropping into the third tier.
Their captain and Worcester wing David Lemi said: "This was a big opportunity for us to have a good ranking before the World Cup draw and credit to the boys today, we came out on top.
"Wales did the same thing they used in the Six Nations and against Argentina. We knew if you stop their go-forward men, you stop their game."
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