A petition signed by 1,000 people failed to prevent Worcestershire County Council's cabinet from deciding to close the school.
None of the councillors involved in Monday's unanimous decision was from Malvern.
Malvern councillor Di Rayner, a governor at the school, did plead for it to be given another chance.
Closure emerged as an option as the school found itself squeezed between falling pupil numbers and a poor Ofsted report, in which it was criticised for failing to provide a good standard of education.
During a consultation meeting earlier this year, parents made it clear that despite the problems, they wanted the school to remain open.
Other options, such as re-opening the school under the Fresh Start programme with a new head, new staff and an injection of funds, federating with another successful school or adopting an improvement action plan were dismissed by the county council.
Spokesman Leigh Shrimpton said: "We're aware how sensitive an issue closing a school is but the educational situation at the school isn't getting any better and the quality of the children's education, now and in the future, is the most important thing."
He said the county council would work with individual families to help meet the needs of children and parents would be able to express a preference for an alternative school.
Acting head Andy Chilman said there was obvious disappointment among families.
"There's a high degree of loyalty and many parents have chosen to keep their children here in spite of the uncertainty," he said
Mr Chilman said the school would be working hard to provide the best education possible for the pupils this year while their futures are being decided.
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