Gerson Rodrigues stunned Portugal in the first half as he fired Luxembourg into the lead at the Stade Josy Barthel on Tuesday.
But Liverpool star Diogo Jota headed home an equaliser before half-time in Portugal's 2022 World Cup qualifying match.
Ronaldo fired Portugal into the lead early in the second half, but the Juventus superstar squandered a brilliant goalscoring chance in the 77th minute.
The 36-year-old Portuguese forward ran clear of the defence and only had Moris to beat in a one-on-one encounter.
However, Ronaldo's shot was easily saved by Moris before the Portugal captain's follow-up shot was denied by the Luxembourg 'keeper's foot.
An onrushing Rafa Silva managed to beat Moris to the loose ball at the edge of the box before his first-time chip found Ronaldo.
Ronaldo scooped the ball into the back of the empty net with a turning side-footed finish, but the Portugal international was ruled in an offside position.
Joao Palhinha added Portugal's third of the match before Maxime Chanot was shown a second yellow for a foul on Renato Sanches.
Portugal are now top of Group A with seven points, but they are level with second-place Serbia.
Portugal will now return to international action in early June with two friendly matches ahead of their Euro 2020 campaign in the same month.
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