The archive touches on the fates of 17.5 million victims of the Nazis and has until now been open only to them and their relatives, a limitation which has led academics to accuse Germany of trying to obscure its past.
"This agreement underscores the importance of coming to terms with history, it underlines the fact that there is still work to be done," German secretary of state in the foreign ministry, Guenter Gloser, said after signing the accord.
The signing ceremony in Berlin followed an agreement struck in April by the 11-nation governing body of the International Tracing Service, part of the International Committee of the Red Cross, which manages the archive in the western German town of Bad Arolsen.
Belgium, the Netherlands and Poland are expected to sign the accord at a later date. Diplomats said there was no political reason for the delay.
The protocol amends the 1955 Bonn Agreements that consigned some 47 million documents to Bad Arolsen, where they take up 27 kilometres of shelf space.
They contain minute, and sometimes macabre, details the Nazi regime recorded about its victims, including a hand-written report stating that 300 people were executed at the Mauthausen concentration camp in Austria on April 20, 1942 as the commander's birthday gift for Hitler.
Another entry reveals that the Nazis kept records of the names of prisoners who had headlice.
For more than 60 years only the families were allowed to obtain information from these files, to the anger of historians, particularly in the United States.
"It is normal that people were scared to open the files. But it is not true that something was being hidden," French ambassador Claude Martin told news agency AFP.
"It was simply a little complicated to get information from Bad Arolsen, but most of what is there was known. Still, it was time to open it to all."
Mr Gloser said researchers wanted to consult the files in the archive to learn what exactly had happened to groups of people who disappeared from particular regions in Europe during the Holocaust.
The amendment to the Bonn Agreements comes in the twilight years of the last generation of Holocaust survivors, after a long debate in Germany about whether opening the archives could prove painful to them.
The files, for example, contain inscriptions by Nazi officers branding concentration camp prisoners and forced labourers as "schizophrenic" or "homosexual".
"On this score, we have reached a compromise between the public's right to know and the victims' right to privacy," Mr Gloser said.
It means that in all countries that signed the protocol, researchers will have to respect the local privacy laws in respect of victims who are still alive.
The existing staff of some 300 at Bad Arolsen will be given additional help and new funding from mid-September to prepare them to cope with the new demand from researchers.
But the decision to open the archive has prompted the departure of Charles Biedermann, a German who ran the International Tracing Service for more than 20 years.
He was opposed to the move out of concern for the privacy of victims.
It is not clear who will replace Mr Biedermann or exactly when Bad Arolsen will open its doors to academics.
The protocol still has to be ratified by Germany and some of the other 11 signatory states before the archives can formally be opened.
A spokeswoman for the German foreign ministry said the signatories had however agreed that this should happen "as soon as possible. Maybe by the end of the year."