Flags on public buildings were raised at 9am on Wednesday as the period of mourning for Sheikh Khalifa ended.
The Ministry of Presidential Affairs said the 40-day period concluded on Tuesday night.
Sheikh Khalifa died on May 13 at the age of 73.
Work across the country was suspended for three days immediately after his death.
Flags had remained at half-staff since. This period was intended as a mark of respect and life across the UAE took on a more sombre tone.
Sheikh Khalifa was the country's second president after UAE Founding Father, the late Sheikh Zayed bin Sultan Al Nahyan.
Sheikh Mohamed was elected President by the Federal Supreme Council last month.
Sheikh Khalifa remembered: in pictures
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Nasser Al Nowais, chairman of the Rotana Hotel Group, with the late President, Sheikh Khalifa. 'He cared about the well-being of people not only in the UAE, but all over the world,' says Mr Al Nowais. Photo: Nasser Al Nowais -
Sheikh Khalifa in Dubai in 1971. Magnum Photos -
An undated photo of Sheikh Khalifa. Wam -
A young Sheikh Khalifa (seated). Wam -
UAE Founding Father, the late Sheikh Zayed bin Sultan Al Nahyan, and his son Sheikh Khalifa watch a military parade in 1978. Photo: Al Ittihad -
Sheikh Khalifa. Wam -
Sheikh Zayed, centre, and Sheikh Khalifa seated to his right. Wam -
Sheikh Zayed and Sheikh Khalifa. Wam -
Sheikh Zayed and Sheikh Khalifa. Photo: Al Ittihad -
Sheikh Zayed inspects plans for the Sheikh Zayed Grand Mosque with his sons Sheikh Khalifa and Sheikh Sultan. Photo: Al Ittihad -
Sheikh Khalifa, left, greets Jordan's King Abdullah in Abu Dhabi on May 16, 2000. Wam -
Sheikh Khalifa and Sheikh Zayed. Wam -
Sheikh Khalifa performs Umrah. Wam -
Sheikh Khalifa and Sheikh Mohammed bin Rashid, Vice President and Ruler of Dubai. Wam -
An image of Sheikh Khalifa is projected on to a building in Abu Dhabi. Antonie Robertson / The National -
President, Sheikh Mohamed, left, with Sheikh Khalifa in 2009. Philip Cheung / The National -
Sheikh Khalifa watches the first Abu Dhabi Grand Prix at Yas Marina Circuit on November 1, 2009, with Nursultan Nazarbayev, president of Kazakhstan, and Sheikh Humaid bin Rashid Al Nuaimi, Ruler of Ajman. Ryan Carter / The National -
Sheikh Khalifa attends National Day celebrations at Zayed Sports Stadium on December 2, 2011. Philip Cheung / Crown Prince Court -
The UAE football team meet with Sheikh Khalifa on Saturday, January 19, 2012, after their 2-1 victory over Iraq in the Gulf Cup final in Bahrain. Wam -
Britain's Queen Elizabeth and Prince Philip with Sheikh Khalifa at Windsor Castle, England, on April 30, 2013. Reuters -
Sheikh Khalifa. Wam -
Sheikh Khalifa with Sheikh Mohammed bin Rashid, Vice President and Ruler of Dubai, Sheikh Dr Sultan bin Muhammad Al Qasimi, Ruler of Sharjah, Sheikh Humaid bin Rashid Al Nuaimi, Ruler of Ajman, Sheikh Hamad bin Mohammed Al Sharqi, Ruler of Fujairah, Sheikh Saud bin Rashid Al Mualla, Ruler of Umm Al Quwain, and Sheikh Saud bin Saqr Al Qasimi, Ruler of Ras Al Khaimah. Wam -
Sheikh Khalifa at Al Bateen Palace, Abu Dhabi. Wam
