Sarah Cope, 36, and Clare Phipps, 26, had their nomination to stand as MPs in Basingstoke rejected by the returning officer before May's general election.
They appeared at the High Court in London in a bid to overturn the returning officer's decision.
Ms Cope said they wanted to change the culture of Westminster where "over 450 of the 650 MPs in Parliament are men".
The two candidates planned to share one seat as Ms Cope is the main carer for two young children and Ms Phipps suffers from a disability.
The acting returning officer rejected their nomination as invalid because two people were seeking election in one seat.
Ms Cope and Ms Phipps had argued the rejection breached both human rights and equality laws.
However, Mr Justice Wilkie ruled the returning officer's decision was "unarguably correct" and dismissed their application.
He said there was "no doubt" they were serious issues but added they were "not proper issues for the court to debate".
Speaking after the ruling, Ms Phipps said: "The support we have received for this campaign, from across the political spectrum and electorate, shows just how important this issue is."
"The court has in effect passed the buck back to parliament."
Previously, Ms Cope said: "The 32 million UK women make up 51% of the population. At the moment however, over 450 of the 650 MPs in Parliament are men.
"We need to change the culture of Westminster and stop wasting so much untapped talent. Allowing MPs to job-share is a relatively minor change which could bring about huge benefits."
Ms Phipps job shares a position on the Green Party executive and is researching gender and health as part of a part-time PhD.
Since 2009 she has suffered from a disability known as idiopathic hypersomnia, a chronic condition which means she sleeps for around 12 hours a day.
Counsel for the Green Party members said they had not been trying to overturn the re-election of Maria Miller, who won the Basingstoke seat in the general election.
Two Green Party candidates have been refused a judicial review over their plans to become job-share MPs.