The building in Dee Street closed in August because of flooding caused by a faulty washing machine.
The synagogue - the most northerly in the UK - will now be repaired after the Jewish community in the city raised more than £10,000.
Repairs are due to get under way on Monday, with the synagogue and community centre expected to re-open early in 2018.
Services have been temporarily held in the home of a congregation member, with chairs provided by the city’s mosque.
Mark Taylor, honorary president of Aberdeen Synagogue and Jewish Community Centre, told BBC Scotland: “We now have reached our £10,000 target.
“We will get it fixed and we will continue to have a Jewish community in Aberdeen.”