The deceased were identified as 25-year-old Hussein al-Amour and 28-year-old Abdul Haleem al-Naqa, the Palestinian health ministry said.
"We will not give up our duty to the blood of the martyrs shed by the occupation, and we know how to respond to this unsafe escalation", Islamic Jihad said in a statement.
Israel's military confirmed the strike, saying the tank fire came after its troops detonated an explosive device that had been placed near the border fence.
Since then, Israel has been preparing for possible attacks by sea by Hamas, especially as the IDF has improved its ability to detect and destroy Hamas tunnels under the fence separating the Gaza Strip from Israel. No injuries were reported in the Saturday morning incident.
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"The IAF attacked terrorist targets deep inside the Gaza Strip last night".
Since March 30, tens of thousands of Palestinians have taken part in weekly protests which Israel says are orchestrated by Hamas and used as cover for attempted terror attacks and breaches of the border fence.
No Israelis have been killed in the clashes.
On May 14 - the bloodiest day of the conflict coinciding with the US's highly-contested embassy move from Tel Aviv to Jerusalem - at least 60 Palestinians were killed by IDF live fire.
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Earlier in May, some 300 burning kites were flown from Gaza across the Israeli border sparking several small fires in Israeli fields, the Times of Israel reported.
The death of the baby inflamed Palestinian passions and led to a deluge of condemnation against Israel for its heavy-handed response to the border protests.
According to Israeli media, the defence ministry ordered the construction of the barrier in the aftermath of the 2014 war with Gaza and after discovering that Hamas fighters had successfully entered Israel by sea.
The Al-Quds Brigades group, which is linked to the the Islamic Jihad organisation, said it would retaliate for the killings, Haaretz reported.
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