One of the targets, in the southern town of Rafah, was a facility of the Islamist movement's military wing, the Ezzedine al-Qassam Brigades, the sources said.
He called on the United Nations and other global bodies to protect the boat leaving from the enclave run by Palestinian resistance movement Hamas.
The Gaza Strip will set off a flotilla of ships on Tuesday in a bid to break the 12-year-long Israeli blockade on the Palestinian territory. Islamic Jihad operates with a measure of independence from Hamas.
Home to almost two million Palestinians, the Gaza Strip has been reeling under a crippling Israeli blockade since 2006 when Palestinian resistance group Hamas was voted to power in a parliamentary election.
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. A spokesperson for the Iran-backed terrorist group confirmed the men were members of its military arm.
The Israeli military said in a statement that its "fighter jets struck military targets in a compound belonging to the Hamas terror organisation in the southern Gaza Strip". "IDF troops arrived at the scene and fired towards the suspects, who fled back into the Gaza Strip", an IDF spokesman tweeted at around noon on Saturday. No injuries were reported in the incident.
The violent demonstrations were meant to end on May 15, but Hamas leaders have said they want them to continue.
There have been no Israeli casualties along the Gaza frontier, but Israel has reported extensive damage to farmland on its side of the border from firebomb-bearing kites flown over from Gaza.
It accuses Hamas, with whom it has fought three wars since 2008, of seeking to use the protests as cover to carry out violence.
The demonstrations came to a head on May 14 when the USA moved its embassy to Jerusalem and at least 60 Palestinians were killed in clashes - nearly all of them Hamas members, the terror group has acknowledged.