President Sheikh Mohamed led the congratulations as Pakistan marked its 78th Independence Day on Thursday.
The UAE leader sent a message of support to Pakistan President Asif Ali Zardari in honour of a milestone moment in the country's history.
Sheikh Mohammed bin Rashid, Vice President, Prime Minister and Ruler of Dubai, and Sheikh Mansour bin Zayed, Vice President, Deputy Prime Minister and Chairman of the Presidential Court, also extended their best wishes in similar messages to Mr Zardari and Prime Minister Shehbaz Sharif.
Pakistan Independence Day is observed on August 14 each year, celebrating the date on which the country declared its separation from British rule.
Power was transferred to Pakistan's founding father, Muhammad Ali Jinnah, on August 14, 1947, by Lord Louis Mountbatten, the last viceroy of British India and the first governor-general of the Dominion of India.
The UAE and Pakistan enjoy deep-rooted ties stretching back to the formation of the Emirates.
About 1.7 million Pakistani citizens live in the Emirates, the second largest expatriate population in the country.
Thousands of people took part in a large-scale Independence Day event held at Expo City Dubai on Sunday, which was attended by Sheikh Nahyan bin Mubarak, Minister of Tolerance and Coexistence.
Sheikh Mohamed regularly holds talks with Pakistan's leadership to help further bolster the robust partnership between the countries.
In June, the head of state met Mr Sharif in Abu Dhabi.
Discussions focused on the economic, investment and development sectors, in addition to regional and international issues.
