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.
"Records are my motivation," Ronaldo had told reporters on Wednesday.
"I want to become the most capped player in history. That would make me proud.
"But it doesn't stop there, I still want to be called up very often."
Ronaldo made his international debut in 2003 and became the first man to score in five World Cups last year before Portugal lost to Morocco in the quarter-finals.
He is currently playing for Saudi club Al Nassr after an acrimonious end to his second spell at Manchester United.
Ronaldo's appearance off the bench in the defeat by Morocco equalled the previous mark of 196 caps held by Kuwait's Bader Al-Mutawa.
He left the pitch in tears following Portugal's shock 1-0 loss against the North Africans.
Since leaving Europe, Ronaldo has scored nine goals in 10 matches for Al Nassr.
He was replaced as the starting striker by Goncalo Ramos during the World Cup, with the Benfica youngster scoring a hat-trick in a last-16 win over Switzerland.
- Ronaldo captains team -
But veteran coach Fernando Santos stepped down following the tournament and new boss Roberto Martinez has immediately put his faith in Ronaldo, who also captained the side.
There were questions over whether his 20-year international career had ended in Qatar as Ronaldo will be 39 by the time Euro 2024 kicks off.
But Martinez, who left his role as Belgium coach after the World Cup, has strongly defended his decision to keep Ronaldo in the fold.
"To be in the national team, you have to be committed," the Spaniard said on Thursday.
"It's a new cycle. It is very important that a player shows commitment and that he can use his experience.
"Cristiano has that: a lot of experience and a lot of commitment to the national team."
Portugal made the perfect start to their qualification campaign with a straightforward win against Liechtenstein.
Cancelo scored the only goal of the first half in the eighth minute but the floodgates opened after the break.
Bernardo Silva doubled the advantage less than two minutes into the second period before Ronaldo hammered a penalty into the bottom corner.
A powerful free-kick from the edge of the box flew through the hands of goalkeeper Benjamin Buchel to complete the scoring.
Ronaldo was substituted late on for Ramos, with the much expected changing of the guard put on the back burner.
Ronaldo adds the international appearance landmark to an impressive list of individual records.
He is the leading goalscorer in European Championship finals with 14 goals and has netted a record 140 times in the Champions League.
Ronaldo has also finished as the top-scorer in three of Europe's top five leagues -- in England, Spain and Italy.
Portugal will visit Luxembourg in their second Group J qualifier on Sunday.
They have also been drawn alongside Bosnia and Herzegovina, Iceland and Slovakia.