The military said the Palestinians approached the fence today and damaged it, posing an "imminent danger." The army said "a hit was confirmed" on both, but refused to elaborate.
It was unclear if the Palestinians were militants or civilians.
Palestinian officials in Gaza had no immediate comment on the shooting incident, and there were no immediate reports of casualties.
Israel considers the Gaza Strip a hostile entity because the militant Islamic group Hamas rules there, and because militants in the seaside territory have carried out attacks on Israel.