Witnesses and Palestinian security officials said one rocket struck near the West Bank Jewish settlement of Maaleh Adumim, while a second hit close to an Israeli military prison near Ramallah.
"Four rockets were fired at Jerusalem, of which two landed in open areas and two were intercepted," an army spokesman told AFP, without giving further details.
Police confirmed the two rockets not intercepted had hit open areas near Maaleh Adumim and in the Ramallah area.
Both the Islamic Jihad and Hamas issued statements taking responsibility for the rockets fired at Jerusalem.
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It was the second time in two days that air raid sirens had sounded across the Holy City as Israel and Hamas militants were locked in a fresh round of bitter fighting in and around the Gaza Strip.
Three loud blasts could be heard around the city shortly after sirens wailed, sending people scrambling for shelter, AFP correspondents said.
Sirens also sounded across Maaleh Adumim, and an explosion was heard in Ramallah, witnesses and a correspondent said.
The rocket hit near a cluster of shacks belonging to the Bedouin Jahalin tribe, causing however no damages or injuries, the witness said.
Further north, Palestinian security sources said a rocket had struck open ground near Ofer, an Israeli military prison that lies to the west of Ramallah.