The Portuguese came from behind three times as Ronaldo, who also set a tournament record of 17 appearances, finally rediscovered his touch to help Portugal make the last 16, where they will meet Croatia in Lens on Saturday.
Group F winners Hungary finished above Iceland, who also qualified after a last-gasp 2-1 win over Austria in Paris, and third-placed Portugal.
Hungary will play the Group E runners-up, which will be decided later on Wednesday between Belgium, Sweden and Ireland, while Iceland will face England.
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Ronaldo equalised twice in the second half after Zoltan Gera's early strike was cancelled out by Nani just before the break. Hungary captain Balazs Dzsudzsak had twice put his side ahead before Ronaldo burst into life with a double strike.
(Editing by Ken Ferris; Editing by Ian Chadband)
