The 27-year-old gave a captain's performance with the winner late in the second-half to lead his side past the uninspiring Czechs into a semi-final against either Spain or France
The Real Madrid star headed home the only goal of the game with 11 minutes left on the clock to seal a narrow victory for the Seleccao and set up a date with either Spain or France on June 27.
Both sides seemed reluctant to over-commit in attack in a cautious first half, though Ronaldo would come closest in first-half injury time with a low drive that rebounded off the post.
Portugal took control in the second half, sending in a number of shots at Petr Cech's goal, but were largely frustrated in their attempts to breach a Czech defence which had conceded the most goals of any team in the quarter-finals.
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The only change for either side was the inclusion of Vladimir Darida ahead of Daniel Kolar in midfield for the Czech Republic, who also named captain Tomas Rosicky as a substitute for the second game running amid concerns over an Achilles tendon injury.
In front of a sizeable fan presence inside the National Stadium, the Czechs just about managed to claim the upper hand during the initial exchanges, as their control of possession restricted Portugal’s enterprise to forays forward on the counter.
Nevertheless, the first hint of an opening fell to Joao Moutinho after 13 minutes, with the Porto midfielder squeezing in a shot on the turn that was comfortably snatched by Cech.
It was a half-chance at best, and illustrative of the cagey beginning to the match, which saw both sides struggle to really stamp their authority on proceedings.
Ronaldo appeared to force Cech into action with a powerful drive after racing into the box, but the chance was quickly snuffed out by an offside call.
Nani and Miguel Veloso were then both booked within minutes of each other after a pair of thumping challenges on Darida and David Limbersky.
Slowly, Portugal would begin to make an improved contribution to the game, eschewing their long-ball approach for a more concerted offensive effort, with Ronaldo, as ever, at the heart of things.
The Real Madrid star went close with an audacious overhead kick that flashed just wide following a struggle by the Czech defence to clear a corner, before seeing a 30-yard free kick miss the target.
However, the Seleccao were handed a blow with 39 minutes gone when Helder Postiga limped off clutching his hamstring, with Hugo Almeida coming on in his stead.
The change did not faze Portugal too much however, who went closest to snatching the lead on the stroke of half time. Ronaldo collected Fabio Coentrao's cross perfectly on the turn, and drilled a low attempt that bounced agonisingly off the base of the post after the slightest touch off Cech's boot.
Ronaldo would come close once more a few minutes after the restart, with another long-range free kick bouncing off the woodwork via a save by Cech.
Portugal were looking the superior side as the second-half unfolded, with Raul Meireles sending a pair of efforts over the bar, before Nani forced Cech to parry his low drive away from goal.
The Chelsea goalkeeper had to be alert once more to tip over a piledriver from Moutinho at full stretch, as the match crossed the hour mark with the Czech Republic struggling to get a sniff of the ball.
Meireles snatched at an opening from just inside the box, before slipping in Nani, whose deflected effort came close to looping into the top corner.
But just when it looked like there would be no way through for Portugal, up stepped Ronaldo to bounce a punishing header into the back of the net after a great cross from Moutinho.Pereira nearly increased the Seleccao's advantage within moments with a well-taken drive, but Cech was equal to it and expertly tipped wide.
But Czech Republic's subdued second half continued as they simply could not find a way back into the match despite a late surge from Cech to the opponents' box for a corner, failing to come close to an equaliser as their tournament ended with a whimper.