Ronaldo's 199th cap came during Portugal's 3-0 win against Bosnia and Herzegovina, with Bruno Fernandes scoring twice and Bernardo Silva notching his 10th international goal.
Bruno Fernandes set up Bernardo Silva who opened the scoring with a chipped effort in the 44th minute
Fernandes added a second through a 77th minute header and a third in the closing stages with a sweet strike.
Ronaldo had a first-half header ruled out for offside at Estadio da Luz.
Portugal stay top of Group J having won all three of their matches.
Coming into the fixture in Lisbon, Al Nassr's Ronaldo, 38, had scored four goals across two European Championship qualifiers in March.
He was fractionally offside when he nodded home Joao Cancelo's cross in the 23rd minute, but Portugal were able to canter to victory without their talisman among the goals.
Bosnia-Herzegovina are now fourth, four points behind second-placed Slovakia.
The visitors could have taken the lead midway through the first half but Edin Dzeko volleyed over when unmarked in the box.
Cristiano Ronaldo was involved in a bizarre altercation on Saturday night after a supporter preceded to run onto the pitch and pick up the five-time Ballon d'Or winner.
It came during Portugal's 3-0 win against Bosnia and Herzegovina, with Bruno Fernandes scoring twice and Bernardo Silva notching his 10th international goal.
Despite much uncertainty shrouding his international career following the Selecao's disappointing exit from the 2022 World Cup, the 38-year-old was selected as part of Roberto Martinez's Portugal squad for this summer's Euro 2024 qualifiers.
It came as many thought the Al-Nassr star would retire from international football after they were beaten in the quarter-finals of the Qatar World Cup by Morocco.
He might have failed to get on the score sheet tonight but was involved in a strange moment as a fan ran on to the pitch to embrace him.
Ronaldo remained motionless as he was grabbed by the spectator who seemed to give the former Manchester United forward a bear hug, before bowing down in front of him, all while holding a Portugal flag.
Seeming to be equally confused by the incident, Ronaldo stood as the pitch invader rose to his feet once again. Wrapping his arms around the Portuguese striker he preceded to hoist him a couple of feet into the air, in a rather comical moment, before dropping him back onto the floor.
Standing face to face, the pitch invader then performs his 'Siu' celebration with Ronaldo, who also joined in, throwing his arms down towards the ground.
The supporter then quickly sprinted away to evade the encroaching security guards. A strange, yet, humorous incident to say the least and hats off to the forward, who smiled and shook the hand of the spectator.