An Israeli army spokeswoman said the two were killed while they attempted to approach a Jewish settlement late on Tuesday night.
"Israeli soldiers spotted two Palestinians who were approaching the Jewish settlement of Brakha, south of Nablus, opened fire on them, killing one and wounding the second," she said.
The spokeswoman said the injured man later died of his wounds and added that they had been carrying Kalashnikov assault rifles.
Palestinian security sources said there had been an exchange of fire between Israeli occupation troops and Palestinians in the area.
The killings come amid a recent lull in violence in the region following Palestinian leader Mahmud Abbas' initiative to re-start peace talks with Israel.
Abbas has deployed Palestinian security forces along the border to prevent Palestinian resistance fighters from firing rockets into Israel. He has also extracted a pledge from the groups to maintain an unofficial truce.