The House of Lords rejected the key amendment, challenging government figures on the cost of registering younger voters, by 263 votes to 246.
The government had overturned a previous change to the EU Referendum Bill, seeking to lower the voting age to 16, saying it would cost 6 million pounds.
Its victory marks the end of the UK parliamentary row over the legislation.
British Prime Minister David Cameron welcomed the news in a tweet, saying: "A key manifesto commitment delivered as the EU Referendum Bill clears Parliament. Voters will have an in/out choice before the end of 2017."
The UK government invoked financial privilege rules, estimating the changes would cost 6 million pounds to implement, which can be used by the Commons "as grounds for overruling any House of Lords proposal that has cost implications".
The government has also said it would be wrong to change the "tried and tested" election franchise for a single poll.
But Labour, the SNP and Liberal Democrats all favoured allowing 16 and 17-year-olds - who were allowed to take part in last year's referendum on Scottish independence - to vote on whether to remain in the EU.
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