One of the missiles -- Grads fired from Gaza -- exploded in a street damaging a synagogue and other buildings. A second missile hit an open area, causing panic but no damage.
A Grad missile was fired at Ashdod late Tuesday, Operation Cast Lead two years ago.
Seven mortar shells fired at the Eshkol and Sha'ar Hanegev regions in the western Negev exploded in open areas, causing no damage or injury, the army said.
Schools, day care centers and kindergartens remained closed in Beersheba Wednesday, Israel Radio reported.
Shortly after the missile attacks, the army responded, targeting Palestinian terror squads in Gaza, the army said.
Islamic Jihad claimed responsibility for the missile attacks and issued a statement saying, "This is an initial reaction to the Zionist crimes against our people in Gaza," Ynetnews.com reported.
Ma'an news agency said the military strikes targeted a neighborhood east of Gaza City. The agency said an Islamic Jihad operative was injured in the strike.
"We may have to consider a return to [Operation Cast Lead]," deputy Prime Minister Silvan Shalom told Israel Radio. "I say this despite the fact that I know such a thing would, of course, bring the region to a far more combustible situation."
The Wednesday attacks occurred a day after at least eight Palestinians including young children were killed in a series of military strikes by the Israeli army in response to earlier missile and rocket attacks on southern Israel.