Alex McLeish made six changes to the side which performed abysmally in the 2-1 Nations League defeat to Israel on Thursday night and they performed competently in a half-full stadium only for debutant Helder Costa to score for the visitors just before the break.
However, the 2016 European Championship winners, who had an even more unfamiliar look about them, doubled their lead in the 73rd minute through Eder before Bruma fired in a third with six minutes remaining with Steven Naismith scoring at the death to put a better sheen on the scoreline.
Scotland face Albania away and Israel at home next month in their final Nations League Group C1 games and McLeish, whose side have three points from two games, will have to find some answers if they are to reach the play-offs, which offer the chance of reaching the 2020 European Championships.
McLeish needed a decent performance to take some heat off following the trip to Haifa.
Personnel change was forced upon him as his back-three - John Souttar, Charlie Mulgrew and Kieran Tierney - were unavailable through either injury or fatigue.
Craig Gordon, Scott McKenna, Jack Hendry, Stuart Armstrong, James Forrest and Oli McBurnie were brought into the side which was set out in a 4-4-2 formation.
However, Portugal were far from full strength.
Head coach Fernando Santos was without their talismanic striker Cristiano Ronaldo, midfielder Bernardo Silva and defender Pepe.
And only defender Cedric and Ruben Dias retained their places from Thursday’s 3-2 win away to Poland in the Nations League with Wolves forward Costa handed his debut.
There was no real hint of a goal until the 15th minute when Portugal captain and keeper, Beto, had to make a fine reaction save from his own player, Sergio Oliviera, after the Porto midfielder had headed towards his own goal after a Forrest cross which had popped up into the air.
McKenna and Naismith had headers which failed to trouble Beto before Portugal threatened through Bruma whose deflected drive just missed the target.
In the 36th minutes Naismith’s header from a tempting Forrest cross missed the far post by a yard.
Five minutes later at the other end, Portugal striker Eder escaped McKenna inside the box and fired in a right-footed drive from 12 yards which was beaten away to safety by Gordon.
All the Scots’ good work, however, was undone with two minutes of the first-half remaining when Bruma set up Kevin Rodrigues and his cut-back was knocked into the net from six yards by Costa who got in front of skipper Andy Robertson.
Scotland started the second-half positively.
Callum McGregor and John McGinn both had attempts on goal before McKenna’s diving header from a McGinn corner just missed the target.
As the inevitable substitutions began to flow the tempo dropped and the game became disjointed.
However, when substitute Renato Sanches floated a free-kick into the Scotland penalty area Eder’s bullet header from 10 yards gave Gordon no chance and there was more misery for the Scots when Bruma raced into the box and hammered a drive high past Gordon, rendering Naismith’s close-range finish a consolation.