The deceased, identified as Hassan Ghazi Nasrallah and Mustafa al-Sultan, were members of Islamic Jihad armed wing Saraya al-Quds, said Health Ministry spokesman Ashraf al-Qedra.
Two Palestinians were killed in the Gaza Strip on Tuesday with authorities in the Hamas-run territory blaming an Israeli strike, but Israel's military immediately denied the claim, AFP reported.
The Israeli army denied any role in the incident and said that contrary to the Palestinian report, the military had not carried out any such drone strike in Gaza.
Soldiers stationed at Nahal Oz military base, along the border with Gaza, opened live fire at Palestinian protesters who approached the border fence, injuring four of them, including two seriously.
It did not say where the rocket fell or report any casualties.
The Israeli military said late Monday it struck Hamas positions in the northern strip overnight in retaliation for a rocket fired at the southern city of Ashkelon, which Israel's Iron Dome missile defense system shot down.
The latest wave of rocket fire followed US President Donald Trump's statement on Wednesday recognising Jerusalem as the capital of Israel.
On Thursday, Israel also targeted Gaza sites with air strikes and tank fire after what a military statement described as "a projectile" was sacked into southern Israel.
Palestinian security officials in the enclave said the sites hit were two Hamas posts.