The procedure has raised concerns over rights violations after the prosecutor handling the case said anyone refusing to submit a sample would be considered a potential suspect.
By the end of the day, 251 of the 527 boys or men who have been asked to participate in the operation had provided samples at Fenelon-Notre Dame, a private Catholic high school in the port city of La Rochelle, on France's Atlantic coast.
"To say this is a first, does not automatically mean it is not a legitimate operation."
It was expected to take until Wednesday for all the required samples to be collected from a total of 475 male students, 31 teachers and 21 other staff known to have been on site at the time of the attack.
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The girl was raped in a toilet at the school on September 30. The lights in the toilet had been turned off and the girl has not been able to identify her attacker.
"We have nothing to go on except the DNA," said Pagenelle. "The choice was simple -- I either had to close the case or do what I have done."
She added: "There is a very strong probability that the person who did this was someone within the school who knew the building."
Each individual asked to provide a sample had to agree to the process and parental consent was also required for the minors involved.
The samples were being taken by saliva swabs under the tongue. They were to be sent to laboratories in Lyon and Nantes and the testing process is expected to take several months to complete.
Pagenelle had raised eyebrows ahead of the testing by announcing that anyone who refused to provide a sample "will become potential suspects who could be taken into custody".
"Refusing to give a DNA sample when not in custody is a right," prominent defence lawyer Joseph Cohen-Sabban told newspaper Le Figaro.