Warning sirens had cut short a rally by Israeli Prime Minister Benjamin Netanyahu as he campaigned on the eve of his Likud party's primaries being held Thursday, public television reported.
The army had earlier said "a projectile was fired from the Gaza Strip towards Israeli territory and was intercepted by the Iron Dome defence system".
Israel's public broadcaster KAN 11 showed images of a security guard informing Netanyahu of a "red alert" late Wednesday.
The prime minister waved goodbye before being hustled from the room with his wife Sarah.
On September 10, the head of the Likud party had also been evacuated from an election rally, in the southern city of Ashdod, after sirens warned of an attack from Gaza.
On Thursday, the embattled premier will face off against longtime rival Gideon Saar in a Likud leadership contest that could threaten his grip on power.
Last week, two rocket attacks were launched against Israel from Gaza without causing injury, Israel's army said.
In response, Israeli warplanes twice bombed Hamas installations in the enclave. Israel holds the Islamist movement responsible for all rocket attacks coming from Gaza, though the Jewish state also targets other armed groups operating there.