Further tries followed with Paul Williams, Kane Thompson and George Pisi touching down, whilst fly-half Tusi Pisi added 12 points.
Matt Giteau scored 18 points for the hosts including a late try, but it wasn't enough to deny Samoa the famous win.
After the game Seilala Mapusua described what the victory meant to the squad.
"It's amazing what adrenalin can do. In the end, the guys were out on their feet. But that's the nature of our team that players are willing to die for the jersey.
"I can only imagine what's going on in the little island a few hours from here. We've always believed that Manu Samoa belongs to the Samoan people, so we're always playing for our people every time we pull on that blue jersey."
Wales face Samoa in Pool D of this year's World Cup in Hamilton on 18 September.