In netting the winner, the Real Madrid forward became the all-time leading goalscorer in European Championship qualification and finals combined, his 23rd strike seeing him overtake Dane Jon Dahl Tomasson and former Turkey striker Hakan Sukur.
It was his 25th goal of the season for club and country, and settled a dour affair which offered little in the way of attacking quality.
That will be of no concern to Portugal, however, who dominated possession for much of the game and finally made the breakthrough in the 72nd minute when Ronaldo forced the ball over the line at the second attempt.
The result leaves Portugal second in Group I, occupying an automatic qualification spot, one point behind Denmark.
Armenia, who defended stubbornly for much of the encounter, remain at the foot of the table with just one point to their name from three matches.
There were notable inclusions at full-back for Portugal, with Jose Bosinwga making his first appearance for four years, while Rapahel Guerreiro took his bow on the international stage.
Portugal had much the better of the opening quarter of an hour, but it was Armenia who had the first meaningful effort on goal when Rui Patricio got down low to his right to keep out Henrikh Mkhitaryan's free-kick after the Borussia Dortmund man had been felled by Ricardo Carvalho.
Ronaldo threatened for the first time midway through the half, seeing his shot parried by Roman Berezovski before blazing the rebound high and wide.
As the game opened up, Patricio was forced into a save by Gevorg Ghazaryan following a swift counter-attack from the visitors.
Portugal continued to enjoy the majority of possession after the interval, and Danny went close to an opener when his looping header struck the top of the crossbar before being held by Berezovski under pressure from Ronaldo.
The forward continued to pose a threat, and duly delivered the telling blow 18 minutes from time.
Substitute Ricardo Quaresma brought a save out of Berezovski and after Nani stabbed the loose ball towards goal, Ronaldo was on hand to bundle over the line.
It was Ronaldo who had netted a stoppage-time winner in the 1-0 victory over Denmark last time out, and he delivered when it mattered once again.
Eder struck the base of the post with a header a minute from time as Portugal went in search of a second, but Ronaldo's goal was enough to secure all three points from what was a laboured performance.
