The first blast rocked the Neve Shalom synagogue, in the central Beyoglu district of the city on Saturday morning.
''It was a huge bang, my windows are full of debris. It shook my stomach," said one eyewitness.
Details of the explosion at the Beth Israel synagogue, 5km from the Neve Shalom site are still emerging.
Turkish television has been showing pictures of injured people being carried away from the blast on stretchers. Many of the injured have reportedly inhaled ammonia and are being treated by doctors.
Although the targets of the attacks are Jewish places of worship, initial reports indicate most of those killed and injured were Turkish Muslims.
Police and local residents say a car ladened with explosives caused the Neve Shalom blast. The attacker is believed to have died in the explosion.
A Turkish group called the Great Eastern Islamic Raiders Front has claimed responsibility for the bombings.
The Israeli Foreign Minister Silvan Shalom has called on the international community to fight against "the forces of evil" following the attacks.
The Neve Shalom synagogue was the scene of an attack by a Palestinian gunman in 1986. Twenty-two Jewish worshippers were killed.
A bomb attack on the same temple, claimed by Lebanese group Hizb Allah, followed in 1992. No one was killed in that incident.