The office had released no statement on the visit, which took place Friday, but it was reported by the Saudi news agency SPA, which said Nayef was cited for his "efforts in the fight against terrorism and extremism".
A Hollande aide said Nayef, who is the Saudi interior minister, received the honour as a "foreign individual, a common protocol practice", noting that Hollande himself received Saudi Arabia's top honour during one of his visits there.
Bilateral ties are strong, sealed by major arms deals as well as Riyadh's participation in the fight against the Islamic State group.
But news of the bestowal of the Legion d'Honneur on Nayef sparked harsh criticism on social media from opponents to the death penalty, many tweeting using the hashtag "#honte" (#shame).
Saudi Arabia on Sunday carried out its 70th execution so far this year, beheading a man convicted of murder.
On January 2, 47 were executed for "terrorism", including Shiite cleric Nimr al-Nimr, a driving force behind protests that began in 2011 among the kingdom's minority Shiites.
Most people sentenced to death in Saudi Arabia are beheaded with a sword.