Fellow forward Helder Postiga also scored twice and Miguel Veloso got another for the home side in the last 20 minutes to wrap up the victory after a 0-0 draw on a swampy pitch in the first leg in Zenica last Friday had left the tie wide open.
Portugal started strongly and Ronaldo showed his intent in the fifth minute with a shot that visiting goalkeeper Asmir Begovic struggled to block.
"I think people are now used to me scoring from free-kicks and it's become one of my specialities," said Ronaldo.
The world's most expensive player was dangerous throughout and had many chances to crown his display with a hat-trick.
Ronaldo sidestepped the keeper to score his second goal after 53 minutes and although the Bosnians had Senad Lulic sent off a minute later, Emir Spahic's 65th minute goal gave them brief hope before Postiga and Veloso struck.
"Congratulations to Portugal, they played faster and better, and I want to wish them good luck in the Euros," said Bosnia coach Safet Susic.
Portugal's qualification follows a remarkable revival under coach Paulo Bento who took over after their dismal start to the campaign and guided them to five straight wins before defeat in the final group match with Denmark left them in the play-offs.
"Qualification was always the objective, but in a difficult context after the first two games as we had no room for error," said Bento, whose knowledge of the players and recent experience as a Portugal international helped to revive their fortunes.
"What leaves me most proud and pleased is that we did so with a strong team spirit," he added.
