The reigning European champions were made to wait for qualification however as Serbia battled to a 3-2 win over Luxembourg in the other game in Group B.
Ronaldo had been substituted in his last two club games by Juventus coach Maurizio Sarri, with the Italian claiming the striker had been struggling with a knee injury.
He reportedly left the stadium before the final whistle after being taken off by Sarri during Juve's 1-0 Serie A win over AC Milan at the weekend.
After a 6-0 win over poor Lithuania, "I knew he (Ronaldo) was able to play," Portugal coach Fernando Santos told Portuguese TV channel RTP.