Abdullah al-Qattati, who was in his 20s, was shot in the chest near Rafah in southern Gaza while treating the wounded and 55-year-old Ali al-Alloul was also killed in the same area, said health ministry spokesman Ashraf al-Qidreh.
It said 200 Palestinians were on the boats but that no one was hurt in the incident.
Israel also killed three people in Gaza, including a 23-year-old heavily pregnant woman and her 18-month-old daughter last Wednesday.
A senior Egyptian official said Cairo was working to secure a comprehensive agreement between Israel and Hamas, beginning with a ceasefire and later including economic improvements.
The protests along the border dubbed have been the greatest threats to Israeli security in the region since operation Protective Edge due to the combination of terror tunnels, riots, attempted infiltrations and the use of incendiary items.
He would be at least the second medic to have been killed by Israeli fire during months of border protests.
The protests came after a deal to end all rocket fire into Israel and air strikes on the Gaza Strip appeared to go into effect around midnight (2100 GMT) on Thursday.
"In light of Hamas statements and the evacuation of Hamas outposts, the Southern Command chose to increase readiness and to close a number of roadways in the Gaza periphery", read the statement released by the IDF Spokesperson's Unit.
The resolution called on UN Secretary General Antonio Guterres to make proposals within 60 days "on ways and means for ensuring the safety, protection, and well-being of the Palestinian civilian population under Israeli occupation", including "recommendations regarding an worldwide protection mechanism".
Hugh Lovatt, Israel-Palestine fellow with the European Council on Foreign Relations, said the "increasingly frequent cycles of escalation and de-escalation" were similar to events before the previous wars.
"Yet their ability to avoid renewed war is becoming increasingly constrained with each cycle of violence", Lovatt added. We condemn in the strongest terms the launching of massive missile attacks into Israel from Gaza and call for an end to violence.
Protesters demand the "right of return" to their homes and villages in historical Palestine from which they were driven in 1948 to make way for the new state of Israel.
Israel hit well over 100 targets across the Gaza Strip in recent days, mostly civilian targets.
The military said Palestinians hurled "explosive devices and firebombs" and in one instance a grenade at Israeli soldiers Friday.
Most were killed by Israeli fire during the protests but others died in air strikes.