Investigating judge Jean-Louis Bruguiere asked that Khaled Ben Mustapha and Ridouane Khalid be held in jail pending inquiries into alleged links with a group suspected of plotting what Bruguiere called "terrorism".
Khalid, 36, was released shortly afterwards.
They and another former Guantanamo detainee, Mustaq Ali Patel, were the last three French citizens held at the base. Four others were returned in July and were still in jail as their case unfolded.
Patel was released without charge on Wednesday, 48 hours after the three arrived in Paris aboard a French military flight.
Khalid has two brothers already under investigation for alleged terrorism-related matters.
Ben Mustapha, 33, who is a married father of two, went to Afghanistan to learn Arabic, according to his family and lawyers.
Patel, who is about 40, was born in India but has French nationality through his marriage to a woman from La Reunion.
He was reported to have been an imam at a French mosque before going to Afghanistan.
There are about 540 detainees from 40 countries at the Camp Delta maximum security facility at Guantanamo. Most were detained after the US-led invasion of Afghanistan.