Geneviève de Gaulle-Anthonioz and Germaine Tillion, who died in 2002 and 2008 respectively, were hailed as heros for their role in the French resistance during World War Two.
In February last year, France's President Francois Hollande announced that they would receive the honour of being buried among the almost exclusively male-dominated "national heroes" entombed there.
His move followed protests from feminist groups and a complaint from an official body for France's monuments urged the president to fix what it called a "wide gender imbalance".
The head of France's Centre for National Monuments said last year that a gender balanced Pantheon could attract more visitors, with only 700,000 visiting the mausoleum every year, far fewer than the likes of the Notre Dame Cathedral, which locks in over 13 million a year.
Only two women are buried there: Nobel prize-winning scientist Marie Curie and Sophie Berthelot, the wife of chemist Marcellin Berthelot.
But in an unusual twist of fate on Friday, it turned out the two resistance fighters won't be buried there after all as their respective families refused to let their bodies be exhumed.
Empty coffins in their honour will be buried at the Pantheon instead, with an urn containing soil from their actual grave sites.
Tillion, an ethnologist who died aged 100, was a founding member of a famed Resistance cell of intellectuals and academics. She was sent to the Ravensbruck concentration camp for women, escaped and eventually wrote an insightful account of her time there.
De Gaulle-Anthonioz, a niece of General Charles de Gaulle, was another Resistance member who was sent to Ravensbruck and also wrote a memoir of that time.