To make things worst, it was the first time the Manu had been held scoreless in 30 Rugby World Cup appearances dating back to 1991.
Samoa trailed 3-0 approaching the half hour mark before two tries in four minutes from Sean Maitland and Greig Laidlaw, and a long-range Stuart Hogg drop-goal opened up a commanding 20-0 lead at half-time.
First five Tusi Pisi was caught napping for the opening five-pointer, with Scottish winger Maitland, who's mother is Samoan, getting on the end of a pinpoint cross-kick from Finn Russell.
Russell was to the fore again four minutes later, stepping inside the tackle of Kane Le'aupepe before offloading to Jamie Ritchie. The flanker fed halfback Laidlaw who bumped off a weak challenge from Tim Nanai-Williams and raced away to score.
The half-time score remain unchanged for 16 minutes but two penalty tries dispelled any hopes of a Samoan comeback, with Ed Fidow yellow carded for illegal entry in the side of a maul before receiving his marching orders six minutes from time for a dangerous tackle, where he slid knee-first into the outstretched Sean Maitland as he dived for the try-line.
Fidow has already received a warning for throwing a punch in their opening match against Russia and will now front a disciplinary hearing in Tokyo on Wednesday.
Head coach Steve Jackson said Samoa were simply outplayed on the night.
"We've got to give credit where credit is due," he said.
"You can be as motivated as you like and they came out tonight and wanted it more and they executed everything that they did. They showed great skill, they moved the ball well, they chanced their arm at times and I thought they played extremely well."
Jackson said the Manu started the second half strongly but were unable to make the most of their opportunities.
"(Our) poor execution is probably due to the fact that they defended extremely well.
"They got off their line and they made their tackles and then they disrupted our ball, which they did extremely well and we couldn't capitalise on that and they turn a ball over then obviously a penalty and a couple of phases later they're under the sticks and we're back to halfway again, so that's probably the frustrating thing," he said.
Samoa were guilty of a host of handling errors which captain Jack Lam partly attributed to the humid conditions under the roof at the Kobe Misaki Stadium.
"To best describe it would be I guess the ball was like a bar of soap. The Scottish probably handled the ball a lot better than what we did and capitalised on that, as you would have seen, and we will take the learnings."
Samoa have now received four yellow cards in two matches, with two of those turning into a red, but Steve Jackson defended the discipline of his players.
"Every team plays to the letter of the law," he said.
"I'm not going to going to talk about the two yellow cards we've received previously but there's been obviously some others that have escaped sanctions that we haven't.
"But these are the decisions that get made by putting yourself in those positions - you're trying to stop two tries and there can be risk and reward but we don't intentionally go out there to get yellow cards and by no means do we coach or train that."
With Rey Lee-Lo and Motu Matu'u still suspended and Ed Fidow set to face the judiciary, Jackson admitted their playing stocks were being well and truly tested with a quick turnaround before their must-win clash against hosts and Pool A leaders Japan on Saturday.
"A couple of those guys are backs and we've got injuries in those positions as well so it's testing but we've got Japan in four days time so there's no point in dwelling on what we don't have. We've just got to move forward with what we've got and pick this group up."
Veteran first five Tusi Pisi said the team was disappointed with the result but more so with the way they played.
"When you lose like this you look at yourself first, so we will be looking in the mirror at ourselves and taking a hard good look at what the individual can improve on and then we'll come together as a team and collectively take the learnings from it."