The Rev Canon Peden, 57, was defeated for the post of Bishop of Glasgow and Galloway by the more experienced dean of the diocese, Dr Gregor Duncan.
An electoral synod comprising 115 clergy and lay church members voted by a majority to elect Duncan, 59, who is also rector of St Ninian's Church in Pollokshields, Glasgow.
Observers said success for Peden would have provided a significant boost towards the first women bishops in the Church of England, where legislation enabling the controversial change may take two years to be enacted.
The head of the Scottish Episcopal Church said the contest had not been decided on gender grounds, but predicted the first woman bishop would be elected before too long.
Another opportunity could be provided by the forthcoming election for Bishop of Argyll and the Isles.
Peden, who was one of three shortlisted for the Glasgow post, is rector of Holy Trinity Church in Stirling; chaplain of Forth Valley College, Stirling; and canon of St Ninian's Cathedral, Perth. She is the first woman to be shortlisted for a bishop since they became eligible in 2003.
Peden was ordained only eight years ago following an academic career in medieval theology, including at Oxford University.
One third of clergy in the Scottish Episcopal Church are women, compared with one quarter in England.
The Most Rev David Chillingworth, Primus of the church and Bishop of St Andrews, Dunkeld and Dunblane, said Peden being shortlisted reflected "the strength of women in the Scottish Episcopal Church".
He said of women bishops: "Today's story is a sign that it's coming."
Supporters of women bishops expressed disappointment at the result.
Christina Rees, chair of the Women and the Church group, said: "It would have been hugely significant and come at a time when I believe churches in Britain are ready."