It means that all cleft lip and palate surgeries will now be centralised in Glasgow, meaning patients will have longer and costlier journeys to receive treatment.
Lothian MSP Miles Briggs had campaigned against the closure of the unit, and earlier this year joined patients in handing over a petition of more than 6,000 names calling for the service to be saved.
He also led a members debate on the issue, and today he criticised the Scottish Government for not listening to the voices of parents and clinicians who called for the surgery to remain open.
Scottish Conservative mental health spokesman and Lothian MSP Miles Briggs said:
“This is one of the worst decisions regarding our health service this SNP Government has taken, and a bitter blow to thousands of patients and their families up and down Eastern Scotland.
“Ministers have completely failed to listen to the views of clinicians, patients and campaigners and have made the wrong decision.
“The Edinburgh surgical unit is led by an internationally renowned surgeon and the audited outcomes it achieves for babies and children are among the best, if not the best, in the whole of the UK. The Health Secretary’s decision now risks the loss of all of this.
“Instead of closing the Edinburgh service, the Health Secretary should have listened and delivered a single service, two-site model with surgery being offered in both Edinburgh and Glasgow.
"This model works extremely well in other parts of the UK and there is no reason it would not be sustainable here in Scotland.
“The families of babies and children living in Edinburgh and Eastern Scotland now face the prospect of longer journeys and extra stresses in travelling to Glasgow.
“From the decisions we are seeing SNP Ministers taking, it is becoming ever clearer that the Scottish NHS is not safe in SNP hands.
“The Cabinet Secretary’s conditions attached to her decision, especially in relation to the surgeon and Lothian outreach clinics, raise more questions than answers and I will be seeking these urgently.”