Housing minister Kevin Stewart has said cuts to the financial transactions which the Scottish Government receives from Westminster is behind the decision.
But the Tories said that Scotland’s budget was “supercharged” by the UK Government and hit out at the decision to end to Help to Buy.
The shared equity scheme has helped more than 17,000 Scots to buy homes with government support since 2013.
Mr Stewart said last summer it would extended into 2021/22 with £55 million of funding allocated to help the purchase of about 2,000 homes.
But the minister has now announced the scheme will be halted in the next week, although £14 million targeting small developers will be retained.
“As highlighted in the Scottish budget, as a direct result of the UK Government’s Spending Review there has been a 66 per cent cut to the Scottish Government Financial Transactions – allocations we receive from the UK Government – with amounts to a reduction of £412m,” he said.
"This means we have had to make difficult choices in how we best use these limited resources to support our shared equity schemes.
“We have protected support for the SME housebuilding sector through retaining the Help to Buy smaller developers scheme with a budget of £14m. However, we are unfortunately unable to continue with the main Help to Buy scheme, and it will close to 2021/22 applications on Friday, February 5."
Current approved applications which have been delayed as result of Covid-19 will still be funded, if the applicant’s financial position remains unchanged.
The scheme focused on more affordable housing with a maximum purchase price of £200,000. About 80 per cent of those who benefited from the programme were under-35.
Mr Stewart added: "A further £10m will fund applications already approved for the main Help to Buy scheme. Therefore this funding will assist more than 4,000 households to buy a home.”
The Scottish Government says its First Home Fund will re-open for 2021/22 applications at the start of April with a budget of £60m, and the Open Market Shared Equity scheme will continue with a budget of £44m.
Scottish Conservatives housing spokesman Alexander Stewart MSP said: “The UK Government has supercharged funding for Scotland spending more than £19 billion to support us through the pandemic.
“We wanted the SNP to produce a budget that placed the recovery over a second independence referendum, but Kate Forbes decided otherwise.
“The SNP found nearly £15m to spend on constitutional policy work, but have refused to continue a scheme aimed at helping people get on the housing ladder.
"It sums up their priorities.”
Help to Buy was targeted on affordable new builds, allowing Scots to buy a new home without having to fund the entire cost.
Participants would pay a minimum of 85 per cent of the home's total purchase price, between the mortgage and deposit, and the Scottish Government held the remaining share under a shared equity agreement.