The Real Madrid forward had twice hit the woodwork and seen his team have a goal chalked out for offside before he arrived on cue in the six-yard box to nod in Joao Moutinho's cross on 79 minutes at the National Stadium in Warsaw.
The Czechs - with captain Tomas Rosicky, the Arsenal midfielder, only on the bench because of an Achilles injury - had started brightly, but lacked a decisive move in the final third.
Portugal, who came through the Group of Death behind Germany, will now face either France or world champions Spain in Donetsk on June 27.
Ronaldo said on BBC1: "We created many chances and hit the post, but it is brilliant for us to have passed into the semi-finals.
"We know it is going to be difficult, but we are ready, we are confident. We are very mature, so we are ready for the fight."
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