The 38-year-old, who was dropped from the Portuguese first-choice XI during the World Cup in Qatar last year, won a 197th cap for his country in Lisbon as a starter. He netted a 51st-minute penalty after earlier goals from Joao Cancelo and Bernardo Silva, before drilling home a free-kick 12 minutes later.
It was Ronaldo's record-extending 120th goal for his country and made him the first man to score 100 times in competitive internationals. Portugal made the perfect start to their qualification campaign with a straightforward win against Liechtenstein.
Ronaldo was substituted late on for Ramos, with the much expected changing of the guard put on the back burner.