Dewi Sant school, in Carmarthenshire, had won first prize at the Urdd Eisteddfod with a rendition of the South African anthem, one verse of which is in Xhosa.
But a day later the festival organisers told the school it had not won because it had broken the Eisteddfod's Welsh-only rule.
Meirion Davies, head of Dewi Sant, criticised the decision, saying the school had sent a copy of the piece it was planning to perform to the Urdd in advance.
He said: "We were not aware of the ruling regarding other languages. In hindsight we should have checked."
Sian Eirian, director of the Urdd Eisteddfod, said: "The Eisteddfod's Welsh rule states clearly that only Welsh can be used on the stage. My sympathies are with the children and their trainers."