Israeli foreign ministry spokeswoman Michal Maayan said the bodies were unearthed by chance by workers in Jerusalem.
"Municipal workers discovered the remains of three Jordanian soldiers near the Sur Baher neighbourhood where a Jordanian army base had been situated," she told AFP.
They will be transported to Jordan overland to be "buried with dignity" in their homeland, Maayan said.
Jordan held east Jerusalem -- where Sur Baher is located -- until June 1967, when it joined Syria and Egypt in a war against neighbouring Israel.
In 1980, the Jewish state annexed east Jerusalem in an act never recognised by the international community.
Israel says the whole city is its united capital, while the Palestinians claim east Jerusalem as the capital of their future state.
In June, Jewish Israelis will celebrate 50 years of what they call the "reunification" of Jerusalem, while Palestinians mark half a century of military occupation.
In 1994, Jordan and Israel made peace, following in the tracks of Egypt, which signed a treaty in 1979.
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