Scores of worshippers attended the prayers and paid emotional tributes in a book placed beside a portrait of the late President.
The ceremony at the Guru Nanak Darbar started at 8pm, and was attended by residents from across the country.
St Andrew's Anglican Church also held special prayers for Sheikh Khalifa as part of its 10am Sunday service.
Worshippers gathered at the church in the Mushrif area of the capital, read prayers and reflected on Sheikh Khalifa's life.
Rev Christine Trainor appeared through video link at the service to read the gospel with people from across the city attending.
Many other places of worship across the UAE from different denominations marked Sheikh Khalifa's death with special prayers.
The UAE is observing a 40-day mourning period, including three days off for the public and private sector, with work resuming on May 17.
Leaders in the region and around the world paid condolences, while some countries have also announced mourning periods.