Last year's FIFA Ballon d'Or winner out-jumped Simon Kjaer to nod in substitute Ricardo Quaresma's cross and give Fernando Santos his first victory as Portugal coach.
Ronaldo had been below-par throughout the Copenhagen clash, perhaps due to a knee niggle that he carried into the contest.
And there was further pain for Denmark as Ronaldo's late goal - his 18th of the season for club and country and 51st at international level - saw them lose for the first time in their qualifying campaign.
Portugal coach Santos took his place on the bench after being granted an appeal hearing by the Court of Arbitration for Sport that temporarily lifted his eight-match reprimand for abusing match officials at this year's World Cup.
Santos, then in charge of Greece, will have liked what he saw early as Portugal kept Denmark goalkeeper Kasper Schmeichel busy.
Ronaldo was first to test him in the seventh minute, stinging the palms of the Leicester City man, before Portugal's talisman almost turned provider in a neat one-two with Danny.
Denmark had appeals for a spot-kick turned down, despite Eliseu appearing to handle the ball in his own penalty area, while at the other end, Nani spurned three chances in six minutes - the best of which saw him head Ronaldo's firm cross over from close range.
After play resumed following Boilesen's substitution, Krohn-Dehli shot wide for the hosts from the edge of the area.
Ronaldo's anger quickly turned to joy, though, as he nodded in from four yards to have the last laugh in the Danish capital.
