Judges found in favour of NHS Greater Glasgow and Clyde which was appealing against a decision of the Court of Session in Edinburgh last year in the case of Mary Doogan and Connie Wood.
The pair had objected to any involvement in the procedure as conscientious objectors but the health board said they should supervise staff involved.
The five justices agreed that conscientious objection is a right only to refuse to take part in activities that directly bring about the termination of a pregnancy.
However, explaining the judgement to the court, Justice Lady Hale urged the hospital to take a sympathetic view, she said: " It is without prejudice to their claim before an employment tribunal that their rights to manifest their religious beliefs and not to be discriminated against because of those religious beliefs may require the hospital to make reasonable adjustments to cater for them."
It had been down to the justices to decide the scope of the abortion act which says: "no person shall be under any duty ... to participate in any treatment authorised by this Act to which he has a conscientious objection".
Both women were employed as labour ward co-ordinators at Southern General Hospital in Glasgow at the time.
Paul Tulley, general secretary, Society for the Protection of Unborn Children, which supported the nurse's case told Premier's News Hour he was bitterly disappointed by the Supreme Court's decision, he said: "For the courts to say that people in this role must be prepared to take part in supervising and helping to manage abortion procedures is deeply disturbing".
Gillian Smith, the director of the Royal College of Midwives in Scotland, said: "This ruling is sensible and both women and midwives will welcome it.
"The ruling gives extensive definition to complex clinical and other situations, in regard to whether conscientious objection applies or not.
"Midwives and other clinicians will benefit from this ruling's clarity and women will be able to continue to exercise their choice over their reproductive rights."
Archbishop Tartaglia said: ""I am dismayed and disappointed at this decision of the Supreme Court which fundamentally impacts on the right of every citizen in this country to follow their conscience in the workplace.
"This was never a case about the rights and wrongs of abortion. Nor was it a case about religion. Rather it was a case which centred on the right of ordinary citizens to have their conscience respected in society and at work. All of society is a poorer, less respectful and less tolerant place as a result of this decision."
Ann Furedi, chief executive of British Pregnancy Advisory Service, said: "We welcome this ruling. bpas supports the right to refuse to work in abortion care, not least because women deserve better than being treated by those who object to their choice.
"But the law as it stands already provides healthcare workers with these protections.
"Extending this protection to tasks not directly related to the abortion would be to the detriment of women needing to end a pregnancy and the healthcare staff committed to providing that care.
"There are enough barriers in the way of women who need an abortion without further obstacles being thrown in their way."
Justice Lady Hale, Supreme Court:
Paul Tulley, general secretary, Society for the Protection of Unborn Children: