The ruling aims to see if the two siblings were born to detainees killed by the military in the 1970s.
Marcela and Felipe Noble Herrera were adopted by the Clarin Group's owner.
The samples will be compared to a genetic database linked to people who disappeared or were killed under military rule.
The Noble Herreras have said the tests violate their privacy, and they have backed their adoptive mother, Ernestina Herrera de Noble, who opposes them.
But they now say they will accept the ruling, rather than appeal.
They say they want to put an end to "the enormous suffering" that they and their adoptive mother have been put through.
The court battle has lasted some 10 years.
Previous samples given by the two have been deemed inadequate for proper testing.
These include blood samples the siblings gave in 2009 at a federal agency, but not the National Bank of Genetic Data.
Their lawyer, Horacio Silva, has now said they will give new blood samples, to comply with the judges' ruling earlier this month.
It's not yet clear when this will take place.
Privacy versus truth?The issue of babies taken from prisoners during the country's so-called Dirty War is a highly emotive one in Argentina.
Several hundred babies are believed to have been taken from their real parents - many of whom were left-wing activists - while they were held at secret detention centres.
These "stolen babies", as they are known in the press, were then given to families loyal to the military during its 1976-83 rule.
Groups like the Grandmothers of the Plaza de Mayo, who campaign on behalf of people who were "disappeared" by the military, have helped a number of children locate their biological relatives.
In 2009, Argentina's congress passed a measure allowing forcible extraction of DNA in such cases, even when the people concerned do not want to discover their past.
The Noble Herrera case has been characterised by some observers as a battle between privacy and "the truth" - whatever that turns out to be - in terms of what should take legal precedence.
Two sets of families whose pregnant daughters were imprisoned, tortured and killed believe Marcela and Felipe are their biological relatives.
They have been trying to prove this through the courts.
The Noble Herrera siblings, meanwhile, claim their rights have been violated.
They say their DNA is private, that they have no desire to trace their biological parents, and that they are victims of political persecution.
In recent years, the media group owned by Ms Herrera de Noble has been staunchly opposed to the current government of President Cristina Fernandez de Kirchner.
In 2009, President Fernandez succeeded in driving through legislation that forced Clarin to sell off parts of its media empire.
The BBC's Vladimir Hernandez in Buenos Aires says the latest development may finally clarify a case that has gripped the country.
If the tests prove the Noble Herreras were indeed taken from detainees, their adoptive mother could face a criminal investigation.
She has always said their adoption was legal.
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