It was pure chance - no one knew about Achilles' weak spot except for himself, his mother, and possibly his mentor, Chiron.
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He shot him in the Heel
Achilles died at Troy when Paris shot him in the heel with an arrow. In some versions of the story, Apollo guides the arrow to Achilles heel. Some versions say the arrow was poisoned. The Iliad ends before Achilles' death.
Paris shot an arrow at him and Apollo guided it to hit Achilles at his only vulnerable spot, the heel.
The youngest son of the king of Troy (he was called Paris)
Paris of Troy killed Achilles in the Trojan war by shooting a poisoned arrow into his heel, the only part of him that wasn't protected. This is where we get the phrase "Achilles heel".