The Manchester United striker started the test match at the Estadio Algarve from close range and was substituted at half time.
The 36-year-old broke Iranian striker Ali Daei’s record of 109 goals last month.
This was Ronaldo’s 181st international match, with which he has now overtaken Sergio Ramos as Europe’s best player.
Malaysian Soh Chin Ann, who retired in 1984, holds the world record at 195.
Jose Fonte scored Portugal’s second goal at the start of the second half on Saturday.
International debutante Rafael Leao, who replaced Ronaldo, hit the wood twice – and Andre Silva scored his third goal in the last minute.
Group A has only five teams and the team that is not playing will play a friendly against the hosts of the 2022 World Cup, Qatar.
Portugal were ousted by a 1-0 win over Luxembourg in Saturday’s qualifying, with Dusan Vlahovic scoring the only goal.
Fernando Santos’ side are one point behind the Serbs but still have one game in hand.