The Christian Action for the Abolition of Torture (ACAT) sought to block the loading of weapons onto the ship through a legal filing on Thursday, arguing the cargo contravened an international arms treaty.
A French judge threw out their complaint but the Bahri-Yanbu moved off the coast of Le Havre shortly after.
It was not immediately clear what had caused the change of plan.
"The boat has left and without its cargo," Laurence Greig, a lawyer representing ACAT told Reuters news agency.
"It is extremely embarrassing for the executive because we thought that we could stop this only with a legal recourse. But while we got a very terse decision against us, pressure from individuals and NGOs led to a positive result."
The legal move by ACAT came weeks after an online investigative site published leaked French military intelligence that showed weapons sold to the kingdom, including tanks and laser-guided missile systems, were being used against civilians in Yemen's war.
Saudi Arabia leads the pro-government military coalition in the four-year civil war that has devastated Yemen, killed tens of thousands and left much of the population on the brink of famine.
France is one of Saudi Arabia's main arms' suppliers, delivering some $1.5bn of weapons to Riyadh in 2017.
On Thursday, French President Emmanuel Macron defended the arms sales, describing Saudi Arabia and the United Arab Emirates as allies in the fight against "terrorism" and saying Paris had received guarantees they would not be used against civilians.