The evergreen 34-year-old scored a first-half penalty and a second-half hat-trick to take his tally for his country to 93, just 16 behind Iranian legend Ali Daei's total of 109.
Portugal's 5-1 win moved the reigning European champion up into the second automatic qualifying spot in Group B, five points behind leader Ukraine.
Since turning 31, Ronaldo has scored 38 goals in 37 games for his country compared to the 55 goals in 123 games prior to his 31st birthday.
It was also the Portuguese talisman's eighth international hat-trick, six of which have come since he turned 31, while Lithuania is the 40th different country Ronaldo has found the net against.
Elsewhere, England beat Kosovo 5-3 in a thrilling encounter as Gareth Southgate's side