Scoring was opened past the 40-minute mark by Bernardo Silva who was set up by Bruno Fernandes. Later, 77 minutes in, Fernandes scored the second point, assisted by Ruben Neves.
Fernandes scored the third point 90 minutes in.
It wasn’t the best match for Bosnia-Herzegovina who are now in fourth place just four points behind Slovakia.
Had Edin Dzeko been successful in his attempt to score midway through the first half, Bosnia-Herzegovina would not have gone home scoreless.
So far, Portugal has won all three of its matches in Group J and remains number 1 in the group rankings.
Ronaldo who has been capped nearly 200 times was offside a fraction when he attempted a score with the help of Joao Cancelo in the 23-minute mark.
The Al Nassr player was also the center of an incident when a fan ran into the pitch to hug him and bowed on his knees.
The fan was quickly taken away by security.