The quakes, two minutes apart, occurred before noon local time and had magnitudes of 3.0 and 4.2, according to the Geophysical Institute of Israel.
The epicenter of both earthquakes was around the Dead Sea, the lowest point on earth, the institute said. The Dead Sea lies on the Syrian-African rift, an active fault line where earthquakes are common.
Tremors also rattled neighboring Jordan, shaking parts of the Jordanian capital Amman and the western city of Salt, the official Petra news agency said. No casualties were reported.
On average, major earthquakes hit Israel once a century. In the past, quakes have caused serious damage to Safed, Jerusalem and the West Bank city of Nablus, and have damaged holy sites, including the Al-Aqsa mosque, Islam's third-holiest site, and the Church of the Holy Sepulcher, sacred to many Christians as the site of Jesus' crucifixion and burial.
The last major earthquake to strike the area was in 1927, with a magnitude of more than 6 and killing 500 people. Israeli experts believe that because of population growth and high-rise construction, an earthquake of the same magnitude today would kill more than 18,000 people.