Mr Malema said the league's remarks damaged its ties with "the mother body" and "we should have known better".
Last month, Mr Malema, 30, said the Botswana government was a puppet regime and a serious threat to Africa.
The ANC - which has already criticised Mr Malema for the remarks - is due to discuss the matter in the coming days.
"We felt it is necessary to apologise and withdraw the statement of the NEC (National Executive Committee) of the Youth League publicly, because we have noted that that statement has poisoned the environment," Mr Malema said on South Africa's state radio SAFM on Sunday.
He also expressed hope that the ANC would accept his apology at its meeting expected on Monday.
"We are a young people who will time and again commit mistakes and are prepared to learn from those mistakes."
The firebrand league leader has been at the centre of controversy before.
He has repeatedly called for the nationalisation of South Africa's mines and farms - striking a chord with the country's poor black population, but unnerving investors.
Earlier this year, he was criticised by South Africa's Afrikaans community for singing a controversial apartheid-era song with the words "shoot the Boer".
Source: BBC
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