Ronaldo scored the winner striking from close range following a goalmouth scramble in the 72nd minute.
"We are in good shape at the moment in qualifying," Ronaldo said. "Denmark also won, but the team is doing very well at the moment, and if we win our game in hand we go top.
"The coach Fernando Santos has been able to impose a new system, bringing new players, and I think we are on the right track."
Elsewhere, Nicklas Bendtner scored twice as Denmark came from a goal down to beat Serbia 3-1. Serbia's Dutch coach Dick Advocaat said after the game that he would consider resigning.
Serbia winger Zoran Tosic opened the scoring with a low strike from 12 yards (meters) in the fourth minute.
But Bendtner equalized in the 60th and centerback Simon Kjaer headed in a free kick from Christian Eriksen two minutes later. Bendtner made it 3-1 in the 85th.
France, which has already qualified as the host of Euro 2016, drew 1-1 with Albania.
In Faro, Portugal coach Fernando Santos made three changes to the side that edged Denmark 1-0 a month ago with the return of veterans Jose Bosingwa and Helder Postiga while leftback Raphael Guerreiro earned his first cap.
Armenia had the best chances in the first half. Henrikh Mkhitaryan had a free kick saved by goalkeeper Rui Patricio and the Borussia Dortmund midfielder then released Kamo Hovhannisyan down the right flank - but Patricio parried the powerful strike from the Armenia wingback.
Roman Berezovski kept Armenia in the game after the break, tipping away a header from winger Nani in the 59th and stopping a long-range attempt from Ronaldo.
However, the Armenia goalkeeper was let down by his defenders when he denied substitute Ricardo Quaresma. Nani flicked the rebound toward Ronaldo, who beat defender Varazdat Haroyan to the ball for the winner.
Portugal nearly added a second in the 89th but the downward header from substitute Eder crashed against the post.
In Belgrade, the match was played in an empty Partizan stadium as punishment by UEFA following a qualifier between Serbia and Albania last month, when skirmishes involving players and fans broke out over an Albanian flag that was flown above the stadium by a drone.
Four minutes after Tosic scored, Serbia almost doubled the lead but goalkeeper Kasper Schmeichel stopped the overhead kick from striker Danko Lazovic.
Tottenham playmaker Eriksen hit the post in the 49th before his low drive was only parried by Vladimir Stojkovic - allowing Bendtner to tap home the equalizer. Two minutes later, Denmark took the lead with Kjaer's header.
The match could have gone either way as Lazovic hit the woodwork in the 64th and Denmark rightback Peter Ankersen rattled the bar with a curling shot a minute later.
Bendtner put the result beyond doubt by chesting down a cross from Michael Krohn-Dehli to beat Stojkovic.
Serbia coach Advocaat was quoted as telling UEFA's website: "This is our first terrible match since I became the manager. If someone should be blamed then it's me. And, yes, I will think about resigning."
In Rennes, Albania defender Mergim Mavraj stunned the hosts with a header in the 40th. But France substitute Antoine Griezmann salvaged a draw by cutting inside to fire into the bottom corner in the 73rd.
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