Ronaldo headed home a cross from Joao Moutinho 11 minutes from the end to set up a semi-final against either world champions Spain or France.
Nani said after the match that the team could even go all the way. "I think if we keep on doing what is necessary we can achieve anything. We have reached the semi-final. That's a dream and we will keep on working for our goal," he said.
It was just reward after another starring performance from the Real Madrid man against opponents who failed to register a single shot on target and were hindered by the absence of injured playmaker Tomas Rosicky.
As is so often the case in knock-out matches in big tournaments, the first half was a cagey affair. Portugal struggled to string two passes together while centre-backs Pepe and Bruno Alves resorted to lumping long aimless balls up the field.
Czech Republic had some joy down their right, with one particularly dangerous cross from Theodor Gebre Selassie only just being cut out by Pepe. Moutinho hit a weak shot from 20 yards that Petr Cech gathered easily.
But then the Ronaldo show really took off. The Real Madrid star sprung into life in the 25th minute as he darted across field, played a one-two with former Manchester United team-mate Nani, shrugged off Michal Kadlec and fired straight at Cech.
It was a rare burst of activity in an up-until-then tame affair but even that wouldn't have counted as referee Howard Webb penalised Ronaldo for pushing. The 27-year-old was only just getting started, though.
On 33 minutes Pepe lobbed a ball into the box and Ronaldo sent an overhead bicycle kick wide of the upright. Next up he sent a free-kick from almost 30 yards swerving wide but in stoppage time at the end of the half he demonstrated his full talent.
Raul Meireles knocked a long ball into the box which Ronaldo controlled on his chest before turning Kadlec and prodding the ball past Cech, only to see it come back off the post.
Portugal increase the pressure
It took Portugal only 20 seconds after the restart to show their intent as Meireles crossed for Hugo Almeida, a first-half substitute for Helder Postiga, who seemed to have pulled a hamstring, but the Besiktas forward headed over when it looked easier to hit the target.
Ronaldo then clipped the outside of the post with a free-kick from fully 30 yards. Moutinho and Meireles combined to play Ronaldo in behind the defence as he came in off his left wing but his finish was skewed high and wide.
Moutinho had an effort from 20 yards on 64 minutes but Cech tipped it over the bar, while Almeida sent another header woefully over. Meireles cleverly played in Nani on 74 minutes but the winger's shot was deflected over the bar.
The goal Portugal's domination richly deserved finally came on 79 minutes as Moutinho made a determined run down the right and produced a peach of cross that Ronaldo headed home on the dive. Full-back Joao Pereira had a chance to seal the match but he shot wide when well placed.