Conditions were difficult with strong wind and heavy rain but the wind did not favour either team, simply swirled around the stadium.
Samoa, fresh from a 24-14 victory over Tonga last weekend, were captained by former Borders number eight Semo Sititi.
The game's five tries were scored by Gordon Ross, Ben Hinshelwood, Ally Hogg, Simon Webster and Mike Blair. However, Samoa were first to put points on the board with a penalty from Roger Warren.
The visitors responded with two penalties from Chris Paterson and Ross' try before half time.
Scotland claimed their second try one minute into the second half. Bruce Douglas was stopped inches from the line, but Ross swept the ball wide for Hinshelwood to grab his first Test try.
A fine pick-up and another half-break from Lamont and drive from MacFadyen took Scotland close before Hogg was driven over for their third try.
Webster and Blair grabbed further tries as the Scots confirmed their dominance.
"It's hard to single players out," said Matt Williams. "I thought the centre combination really worked well. I thought Andy Henderson had his best game for Scotland tonight, both in attack and defence.
"I thought Scott Murray was a real captain and Donnie Macfadyen did really well. It was a great team effort."
Samoa: Vili, Fa'atau, Lima, Tagicakibau, Warren, So'oialo, Lealamanua, Meredith, Leupolu, Lafaiali'i, Palepoi, Vaili, Sititi (capt.), Ulia.
Replacements: Tafunai, Lemalu, Viliamu, Von Dincklage, Senio, Schuster, Lemi.
Scotland: Paterson, Lamont, Hinshelwood, Henderson, Webster, Ross, Cusiter, T Smith, Bulloch, Douglas, Grimes, Murray (capt.), White, Hogg, MacFadyen.
Replacements: Scott, C Smith, Fullarton, Petrie, Blair, Parks, Southwell.
For more details click here.