Mary Doogan, 58, and Connie Wood, 52, argued that being required to supervise staff involved in abortions was a violation of their human rights.
As well as having no direct role in pregnancy terminations, they should also be able to refuse to support staff taking part in the procedures.
The women took their case against NHS Greater Glasgow and Clyde to the Court of Session in Edinburgh but lost last year. But three appeal judges at the same court today ruled that their appeal should succeed.
"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," ruled Lady Dorrian, sitting with Lords Mackay and McEwan.
The health board noted the decision and said it would be considering its options with its legal advisers. Ms Doogan and Ms Wood were employed as labour ward co-ordinators at the Southern General Hospital in Glasgow.
Both women, practising Roman Catholics, registered their conscientious objection to participation in pregnancy terminations years ago, as allowed by the Abortion Act, but became concerned when all medical terminations were moved to the labour ward in 2007.
They argued that previously they had not been called on to delegate, supervise or support staff treating or caring for patients undergoing termination procedures - a stance disputed by the health board.
They said the supervision and support of staff providing care to women having an abortion did amount to 'participation in treatment' and breached their rights under the European Convention on Human Rights.
In a statement, Ms Wood and Ms Doogan said: "Connie and I are absolutely delighted with today's judgment from the Court of Session, which recognises and upholds our rights as labour ward midwifery sisters to withdraw from participating in any treatment that would result in medical termination of pregnancy.
"In holding all life to be sacred from conception to natural death, as midwives we have always worked in the knowledge we have two lives to care for throughout labour; a mother and that of her unborn child.
"Today's judgment is a welcome affirmation of the rights of all midwives to withdraw from a practice that would violate their conscience and which over time, would indeed debar many from entering what has always been a very rewarding and noble profession.
"It is with great relief we can now return to considerations that are all to do with childbirth and midwifery practice and less to do with legal matters."'conscientl