The visitors, coached by Under-19s boss Ricky Sbragia with regular U21 tactician Billy Stark taking control of Scotland against Luxembourg, opened the scoring in the 12th minute.
Somalia-born Feruz headed home from a corner and he netted again in the 21st minute to double Scotland’s advantage.
The diminutive 17-year-old striker outran the Portugal defence to give the visitors a two-goal lead at half time.
However, they were unable to frustrate the hosts for long in the second half with central defender Paulo Oliveira pulling a goal back in the 53rd minute with a free header.
Guinea-Bissau-born Aldair equalised four minutes later despite Scotland’s best efforts to clear the ball off the line.
Portugal were awarded a penalty when Lewis Toshney was adjudged to have handled in the box. Sergio Oliveira’s ensuing spot-kick in the 69th minute proved the match-winning effort.