The European champions equalised when Pepe headed home following a short corner, but Uruguay swept up the field and carved them open once more, with Cavani firing home his second and Portugal unable to respond.
However, Cavani struck a well-placed shot in the 62nd minute to ensure that Portugal moves on to the quarter finals. He was helped to the sideline with his arm around Ronaldo's back.
"And I also want to congratulate the organisation of this World Cup, it has been fantastic in every way; the organisation, the security, the atmosphere is ideal and it must be said".
Portugal coach Fernando Santos told a news conference he hopes Ronaldo will be available for the start of the Nations League in September. "This is the World Cup and we are playing for our national teams".
It is an accusation often levelled at Portugal that they are a toothless team if Cristiano Ronaldo has an off day, but their victory in the Euro 2016 final with their talisman missing most of the game through injury is used as the ideal riposte to that suggestion.
On paper, Uruguay have the stronger team.
It was really unnecessary and Ronaldo deservedly got criticised for it.
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Suarez is a pest, and defends from the front with the same ferocity as Godin and Gimenez 70 yards further back. They carry a huge burden on their shoulders, yet each scored crucial goals in the Group stage.
Being level lasted only seven minutes.
After Uruguay's opening World Cup win over Egypt, Luis Suarez was slammed for a sluggish performance, looking off the pace and as if he was "towing a caravan" around the pitch in Yekaterinburg. Just a few steps inside Portugal's half, Cavani hit Suarez with a pinpoint cross over the top of the back line, and immediately made a run behind the Portuguese defense.
Santos had said: "Cristiano still has a lot to give to football". "Uruguay had never scored like that".
Uruguay set up perfectly to stop him from being the difference maker that he so often is in matches, especially in big matches such as this.
And although Uruguay finally conceded a goal, it was the first this year in the team's seventh match.
Uruguay progressed from their group with a ideal record of three wins from three.