An army spokesman said they had "specific inside information" that Israeli targets were going to be attacked.
"We fired at them, including from the air, and we saw that they were hit," the army spokesman said.
Islamic Jihad confirmed that the fighters were firing rocket-propelled grenades into Israel when the army opened fire on them.
Palestinian sources said another fighter was wounded by Israeli fire during the incident, which took place in a field regularly used by fighters to launch attacks on Israel.
The army spokesman said the gunmen returned fire but hurt no one.
Israeli security forces are on high alert before the general election on Tuesday.