The Juventus forward has now scored 93 international goals, 16 behind Iran legend Ali Daei’s world record.
He scored an early penalty, before Vytautas Andriuskevicius equalised.
The result keeps Portugal in an automatic qualifying place, five points behind Group B leaders Ukraine.
It was an eighth international hat-trick for 34-year-old Ronaldo, who also scored four against Andorra in 2016.
Serbia moved up into third place in the group with a 3-1 win at Luxembourg, with Aleksandar Mitrovic scoring twice.