It was the second night of rocket fire since US President Donald Trump's statement on Wednesday recognising Jerusalem as the Israeli capital.
His declaration sent shock waves through the region, and Gaza's Islamist Hamas rulers called for a new intifada, or Palestinian uprising.
The Hamas-run health ministry in Gaza said that 14 people were wounded, suffering what it described as light to moderate injuries.
Gaza security officials said the targets were in the northern Gaza Strip.
The Israeli military said earlier that its Iron Dome anti-missile system intercepted a rocket fired from the Palestinian enclave.
It said it later detected a second missile launch, but had so far not found any sign that it had fallen inside Israeli territory.
"In response to the projectiles fired at Israel from the Gaza Strip earlier today, Israel Air Force aircraft targeted a Hamas training compound and an ammunition warehouse in the Gaza Strip," an English-language statement said.
A previously unknown Salafist group calling itself the Salahedin Brigades claimed responsibility for the first attempted attack.
But the Israeli army said it held Hamas responsible for all attacks originating from the territory under its control.
On Thursday, Israel responded with air strikes and tank fire into Gaza after what a military statement described as "a projectile" was fired into southern Israel.
Palestinian security officials in the enclave said the sites hit were two Hamas posts.
The Israeli military said the targets were "two terror posts", without identifying them.
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