Scott McTominay shocked the home fans at the Estadio do SL Benfica when he headed the opener in the seventh minute but the home side eventually made sustained pressure count when Bruno Fernandes netted from 20 yards early in the second half.
Scotland came back into the game but the tide turned again and substitute Ronaldo twice hit the post before knocking home a Nuno Mendes cross from close range in the 88th minute to seal a 2-1 win.
It was a third game in a row that Scotland had lost in the closing stages but, just like their opening Nations League A1 match against Poland, there were elements of the performance to admire.
Scotland were unchanged other than Ryan Christie and John McGinn swapping flanks, which meant the continuation of Steve Clarke's experimentation with a back four in the absence of Kieran Tierney.
Clarke's side forced some early corners and they took the lead after Andy Robertson teed up Kenny McLean to whip in a dangerous cross. McTominay timed his run to perfection as he sneaked round the back of the home defence to head home from six yards.
Clarke's side immediately came under the cosh. Some superb penalty-box defending from Scott McKenna in particular kept Portugal at bay but there were close calls throughout the first half.
Rafael Leao was constantly getting beyond Anthony Ralston and threatened on a number of occasions while also setting up Diogo Jota to shoot over. Centre-back Antonio Silva twice headed over after Scotland struggled to get set following short corners.
Chances were coming from all angles. Angus Gunn parried Jota's header after the Liverpool attacker ran off the back of Ralston and Nuno Mendes fired just wide from 25 yards.
The only respite for Scotland came when Lyndon Dykes and McTominay won free-kicks to get them up the park but they failed to make the most of their set-pieces.
The half-time whistle was welcome relief but Scotland came back out to the sight of Ronaldo stripped for action and looking to add to the 900th career goal he netted against Croatia.
The equaliser came in the 54th minute when Leao set up Fernandes to sweep in a first-time strike from 20 yards which spun away from Gunn and into the corner of the net off the goalkeeper's hands.
Ronaldo was firing shots from all angles but Scotland suddenly started to get the ball down and play and got their first efforts at goal since the opener. The hosts had already notched 20.
Ralston and Christie delivered dangerous crosses, the latter had a shot blocked, McTominay forced a save and Scotland forced several corners.
Clarke made changes in the 74th minute when former Sporting Lisbon midfielder Ryan Gauld replaced the limping McLean and Somerset-born Tommy Conway replaced Dykes to make his competitive debut.
Portugal quickly got back on top though. Joao Felix looked certain to score when Ronaldo set him up with a backheel but Gunn threw out a leg to block the Chelsea player's shot.
Gunn pulled off an even better stop from Felix's header before Ronaldo fired the rebound off the outside of the post before heading against the other upright moments later.
But the 39-year-old was soon on hand to net the winner and Scotland could not work the goalkeeper as they pressed for an equaliser.
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