Portugal's Rúben Dias and Raphaël Guerreiro both scored own-goals to put the Germans ahead 2-1 at halftime.
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Portugal has become the first team to score two own goals in one game at the European Championship, handing a 4-2 victory to Germany.
Cristiano Ronaldo initially gave Portugal the lead in Munich but then Rúben Dias and Raphaël Guerreiro both scored own goals, put the Germans ahead 2-1 at half time.
Germany's Kai Havertz and Robin Gosens scored early in the second half for Germany, although Diogo Jota got one back for Portugal in the 67th minute.
Both Portugal and Germany now have three points in the Euro 2020's Group F. France leads with four points but was surprisingly held to a 1-1 draw by Hungary earlier on Saturday.
The Germans will play Hungary in Munich on Wednesday in their final group game. France will face Portugal in Budapest in the other.