The world's most expensive player hit the woodwork twice on an initially frustrating evening but crowned Portugal's dominant second-half performance with his third goal of the tournament, nodding a right-wing Joao Moutinho cross down and into the net.
It was an impressive display from the Portuguese who were appearing in their fifth European Championship quarterfinal in a row and will play Spain or France in the last four.
"It was a fantastic game for Portugal," said man of the match Ronaldo. "In the first 20 minutes we weren't that good but then we improved a lot. We had a lot of opportunities. The Czechs didn't have any - that's a great game."
"I think the chances (of reaching the final) are 50-50 and we just have to believe in it."
Czech Republic coach Michal Bilek added: "Well we knew this was going to be very difficult. Portugal have a great attack. In the second half, we lost our strength and our energy and one situation was enough to decide (the match)."
The Czechs made a lively start inspired by the clever prompting of Petr Jiracek and Portugal took time to settle.
Their simple gameplan was based around getting the ball to captain Ronaldo at every opportunity and he openly vented his frustration when his team mates failed to pick him out.
Ronaldo failed to connect properly with an overhead kick to the delight of the Czech fans, smashed a 35-metre free kick well wide and just before halftime struck the post following a brilliant turn and firm shot.
Portugal's Nani and Miguel Veloso were booked as tempers frayed and they suffered another blow when striker Helder Postiga was carried off injured just before halftime and replaced by Hugo Almeida.
Almeida missed a great chance to open the scoring 19 minutes into the second half when he wastefully headed Raul Meireles's perfect cross over the bar.
Another long-range Ronaldo free kick grazed the outside of the post and the Real Madrid forward then lashed a half-volley over the bar.
Portugal were dominating and Nani forced Petr Cech into a sprawling save before Almeida was adjudged offside when he nodded Nani's cross into the net.
The Czechs earned a brief respite following a brilliant surging run down the left by Vaclav Pilar but Portugal hit back when Joao Moutinho's swerving drive was tipped over by Cech and Nani's shot was saved after good work by Meireles.
The match appeared to be drifting towards extra time when Portugal picked another hole on the left side of the Czech defence and Ronaldo stole in to head the ball emphatically down into the ground with the bounce taking it high into the net.
