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 maintained its 100% start to Euro 2020 qualifying.
England led convincingly at half time, recovering from an early defensive lapse that saw Kosovo take the lead after 35 seconds to go into the break 5-1 up.
Raheem Sterling, Harry Kane, a Mergim Vojvoda own goal and a Jadon Sancho brace -- the teenager's first goals for his country -- gave England a commanding lead following Michael Keane's error that gifted Valon Berisha the opening goal.
But another two defensive errors early in the second half saw the visiting side get to within two courtesy of Berisha's second and Vedat Muriqi's penalty and, in truth, Kosovo could have had more.
Meanwhile, defending world champion France eased past Andorra with a 3-0 victory, despite Antoine Griezmann missing his second penalty in four days.
Kingsley Coman, Clement Lenglet and Wissam Ben Yedder scored for the host, although France drops to second in the table due to its head-to-head record against Group H leader Turkey.