The Real Madrid ace powered a header past the custodian on the 79th minute to send Paulo Bento's men to the semi-finals in a match which was largely dominated by the Seleccao.
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"This is a not a good feeling for us tonight," he told reporters after the game. "We lost, they were better and deserved to win.
"Ronaldo is one of the two best players in the world, and he proved it with that header. He is truly hard to stop."
Portugal will face either Spain or France in the last four, which will be played out on June 27.