Midwifery sisters Mary Doogan, 58, and Concepta Wood, 52, who worked as labour ward coordinators at the Southern General Hospital in Glasgow, had their appeal upheld after losing a previous case against NHS Greater Glasgow and Clyde Health Board (GGC).
Three appeal court judges ruled today that the women can exercise their right to conscientious exemption by refusing to delegate, supervise or support staff looking after women undergoing abortions.
Brian Napier QC, for the health authority, warned at an earlier hearing that the outcome of the case was likely "to have general importance for other hospitals not just in Scotland, but throughout the UK".
Judge Lady Dorrian said today: "In our view the right of conscientious objection extends not only to the actual medical or surgical termination but to the whole process of treatment given for that purpose.
"The right is given because it is recognised that the process of abortion is felt by many people to be morally repugnant.”
The two midwives had their initial challenge rejected by Lady Smith at the Court of Session in Edinburgh last year.
Miss Doogan, of Garrowhill, and Mrs Wood, of Clarkston, objected on religious grounds to participating in abortion and believed the foetus has a right to life.
The pair have a right to conscientious objection, which is recognised in the 1967 Abortion Act.
The women also originally claimed that the stance adopted by the health board also violated their rights under the European Convention on Human Rights.
The pair maintained that before 2007 they were not called on to delegate, supervise or support staff dealing with patients undergoing terminations, although the board denied that.
The court heard that following concerns over the increase in terminations at the labour ward, the women had sought confirmation that as they had expressed a conscientious objection to abortion, they would not be required to be involved in any way in the procedures.
The grievance was not upheld and an appeal to the board was refused.
Rejecting the midwives’ claims in an earlier hearing, Judge Lady Smith said: "They are not being asked to play any direct role in bringing about terminations of pregnancy.
"Nothing they have to do as part of their duties terminates a woman's pregnancy.
"They are sufficiently removed from direct involvement as, it seems to me, to afford appropriate respect for and accommodation of their beliefs.”
Miss Doogan and Mrs Wood appealed against the ruling to the three judges at the Court of Session.
Their counsel Gerry Moynihan QC argued that they should not be required to carry out duties which were, or were liable to be, in conflict with their conscience.
He said that because the midwives let the administration know of their objection in advance, the health board could manage its staff as a whole to respect their right to conscientious objection.
"The administrative convenience of the health board is irrelevant because the right is a balance between facilitating abortion while respecting the genuine conscientious objection of medical, nursing and ancillary staff," he said.
He told the court that the woman said that prior to 2007 there were "work around arrangements".
NHS GGC said in a statement: "We note the outcome of the appeal and will be considering our options with our legal advisers over the next few days."