Samar Khaled, 25, and Yazan Afana, 26, were shot dead during an Israeli raid on Balata refugee camp, east of the occupied West Bank city of Nablus, the ministry said in a press statement.
The number of Palestinians killed by Israeli gunfire since early this year has risen to 140, it added.
The Palestinian Foreign Ministry emphatically denounced the killing of the two young Palestinians as part of a series of field executions executed by Israeli forces against unarmed Palestinians.
The ministry blamed the Israeli government for these premediated crimes that represent an official Israeli policy that only serves election-bearing goals.