The Swedish Labour Court, or Arbetsdomstol, ruled that JönköpingCounty did not discriminate against Ellinor Grimmark unfairly when it decided not to employ her.
"The Swedish Labour Court considers that a portion of the [midwife's] demands are too out-of-date and no longer applicable, and that the midwife has not been able to prove some of her claims," the court said.
The court also judged that "no breach of the midwife's freedom of opinion or expression had been committed".
Ellinor Grimmark, from Jönköping in central Sweden, was refused a summer job at a maternity clinic in 2013 because she objected to assisting in abortions, giving out the morning-after pill, or inserting the contraceptive coil, on the grounds of her Christian faith.
She was subsequently refused positions at two other hospitals in the region.
She told Radio Sweden that she was disappointed by the ruling but not surprised.
"I'm disappointed that it went this way one more time, but we were expecting this and we were prepared for this outcome," she said.
She said she did not understand how excusing her from assisting in abortions would threaten the right of women in Sweden to terminate their pregnancies.
"It is just me and one other midwife in Sweden, so I don't understand how it would contravene the right to have an abortion," she told the TT newswire.
The court ruled that Grimmark must pay Jönköping County's SEK 606,000 legal costs.
If the court had upheld Grimmark's claim, she would have been entitled to compensation for the legal costs she ran up in two earlier cases.
"We think this is extremely positive and had not been expecting anything else," Ann Johansson, deputy chairperson of the Swedish Association of Health Professionals, told Swedish Radio.
Kavot Zillén, a specialist in medical law at Stockholm University, earlier told Swedish Radio that the decision would set a precedent for whether Christian midwives could demand the right not to carry out abortions on grounds of conscience.
Grimmark appealed earlier to Sweden's Equality Ombudsman and then took her case to Jönköping District Court. Both ruled that she had not been subject to discrimination.
Anders Liif, head of human resources for Jönköping county, said before the ruling that employees could not expect to be excused from carrying out the central duties of the job for which they were applying.
Everyone has the right to their personal beliefs, but one can not go from that to yourself defining what work duties you can and cannot carry out," he told Swedish Radio.
"The care we provide is defined by the needs of patients, not those of employees."
Grimmark's case has attracted much attention from the international anti-abortion movement, and she has received financial and legal support from the Alliance Defending Freedom (ADF), a US-based anti-abortion group.
Ruth Nordström, the lead lawyer for Scandinavian Human Rights Lawyers, who is working with Grimmark, aims to take the case to the European Courts.
She told Swedish Radio before the ruling that she aimed to win Swedish midwives the right to work exclusively in maternity wards.
"Abortions are always planned which means that it is possible to solve it simply through work schedules, which is what has been done previously," she said.