The former Manchester United and Real Madrid star followed up efforts from Bruno Fernandes and Scott McTominay to prolong the Selecao's perfect start to League A Group 1, leaving Steve Clarke's spirited troops crestfallen in the process.
Despite becoming the first verified man in history to reach 900 professional goals against Croatia in midweek, Ronaldo was dropped to the bench for the Estadio da Luz encounter, a move that did not initially pay dividends for Roberto Martinez.
Indeed, Scotland took a shock lead through their own clinical talisman in Scott McTominay and somehow made it to half time with their advantage intact, despite a barrage of attacks from a sea of desperate red shirts.
A Portugal equaliser appeared inevitable, though, and so it proved when Bruno Fernandes's scuffed attempt found the bottom corner with a helping hand - or two - from the previously impenetrable Angus Gunn.
The hosts unsurprisingly looked the more likely to nab the game's critical third goal, and so it proved when substitute Ronaldo was presented with an open goal to tap the ball into with just two minutes remaining.
The 901-goal striker had just been denied by the woodwork two times in quick succession before triggering Lisbon pandemonium, which momentarily spilled over onto the field in an unsavoury manner as a pitch invader attempted to obtain a selfie.
That breach prompted further and relevant questions about stadium security, but the Portugal party quickly began soon after, and things are already looking ominous for Scotland in the Nations League big time.
PORTUGAL VS. SCOTLAND HIGHLIGHTS
Scott McTominay goal vs. Portugal (7th min, Portugal 0-1 Scotland)
Who saw this coming? Not the Scotland bench by the looks of things - some of them look as dumbfounded as their Portuguese counterparts!
The visitors load the Portugal box as they play a free kick short on the left-hand side, and Kenny McLean whips a sumptuous first-time cross in the direction of a few white shirts at the back post.
Fruitlessly trying to organise his defence, Ruben Dias has no idea where McTominay is and plays the Napoli man onside, allowing him to nod a close-range header past a static Diogo Costa.
That is 10 goals in 13 international appearances for the former Manchester United man!
Bruno Fernandes goal vs. Scotland (54th min, Portugal 1-1 Scotland)
Portugal's unrelenting pressure finally tells, but for all of his heroics in the first half to keep the hosts at bay, Scotland goalkeeper Angus Gunn will not want to see this one back!
Rafael Leao picks out Fernandes inside the D, and the Manchester United man hits a scuffed shot first time, which manages to find its way into the far corner with the help of Gunn's palms.
The Scotland shot-stopper will certainly feel that he should have done better with that one, but it was only a matter of time before the Selecao hit back.
Ronaldo hits post and Gunn wonder save (82nd min, Portugal 1-1 Scotland)
From hero to zero and back to hero! Gunn barely keeps Scotland on level terms, as Ronaldo is denied career goal number 901 by a matter of inches.
The 39-year-old meets Fernandes's inswinging cross and aims for the far corner with a header, which bounces once and clips the base of the post before flying towards Gunn's goal.
With Joao Felix baring down on him, the Scotland goalkeeper manages to palm the ball away just before Ronaldo's initial effort goes over or Felix can pick up the pieces!
Oh, and he had produced a terrific diving stop from a Felix header just a matter of moments before.
Cristiano Ronaldo goal vs. Scotland (88th min, Portugal 2-1 Scotland)
What was that about goal number 901 for Ronaldo?
The Al-Nassr superstar had the if-looks-could-kill about him after being agonisingly denied by the frame of the goal a few moments before, but he makes no mistake with just two minutes of normal time remaining.
Paris Saint-Germain left-back Nuno Mendes whips in a delightful ball into the six-yard box, which is missed by both Gunn and Diogo Jota, but Ronaldo escapes the attention of Grant Hanley and taps into an empty net.
Cue the siu.
MAN OF THE MATCH - BRUNO FERNANDES
Yes, Ronaldo scored the late winner. Yes, Gunn make a fabulous string of saves to keep Scotland in with a chance of a point or three. But Bruno Fernandes was the metronome that kept Portugal ticking all night long.
The Manchester United captain undeniably got a tad fortunate with his equaliser that Gunn should have palmed behind, but he made six key passes - two of them resulting in big chances - completed all four of his long pass attempts and got stuck in defensively four tackles. The best player on the Lisbon pitch by a country mile.
PORTUGAL VS. SCOTLAND MATCH STATS
Possession: Portugal 69%-31% Scotland
Shots: Portugal 26-5 Scotland
Shots on target: Portugal 7-2 Scotland
Corners: Portugal 12-6 Scotland
Fouls: Portugal 14-7 Scotland
BEST STATS
WHAT NEXT?
Thanks to Croatia's narrow win over Poland in the other League A Group 1 encounter, Portugal now hold a three-point lead at the top of the standings, while Scotland remain at the foot of the pile with zero to their name.
Martinez's men will head to Warsaw to face Poland on October 12, three days before travelling to Scotland, whose next fixture pits them against Luka Modric's Croatia in Zagreb.