Israel transferred the remains of Imad Awadallah, 48, and his 46-year-old brother Adel, to Palestinian officials at a checkpoint in the northern West Bank overnight, Palestinian activists said.
They also handed over the bodies of two others, including a suicide bomber who blew himself up at a Jerusalem restaurant in 2001 during the second Palestinian intifada (uprising).
The Palestinian National Campaign to Return the Bodies of the Martyrs says Israel still holds the bodies of some 29 Palestinians in a special cemetery for "enemy combattants" in the Jordan Valley.
In July 2011, the then defence minister Ehud Barak reneged on an agreement to hand over the bodies of some 84 militants killed since 1967, including the Awadallah brothers.
The defence ministry said such a transfer was inappropriate in light of the captivity at the time of Gilad Shalit, an Israeli soldier who was snatched by Gaza militants in 2006.
Shalit was released later in 2011 in exchange for the release of 1,027 Palestinian prisoners.