The exercises, held every four years, came after a simmering row over ownership of three Gulf islands contested by the Emirates and Iran, and the United States' deployment of cutting-edge F-22 fighter jets to the UAE.
However, French and Emirati military officials insisted on Wednesday that the "Gulf 2012" war games had been scheduled years ago, and that they carry no political messages to any side.
"There is no relation or link between military training taking place and political events, swings, or instability in the region," said Major-General Pilot Rashad Salem al-Saadi, head of the UAE Joint Command and Staff College.
The commander of French forces during the war games, Vice Admiral Marin Giller, also said the exercises had "no link to anything happening in the region."
The exercises were attended by Abu Dhabi Crown Prince Sheikh Mohammad bin Zayed al-Nahayan, who is also the deputy supreme commander of the UAE armed forces.
They took place in the western Al-Hamra desert region near the border with Saudi Arabia and shores of the Gulf, about 250 kilometres (160 miles) from the coast of Iran.
Tehran had in the past threatened to retaliate to a possible military attack over its nuclear drive by blocking the Strait of Hormuz, through which most Gulf oil is exported.
Tensions have been growing across the region as Western powers have been pressing Iran over its nuclear programme.
While the issue is currently the subject of talks, the next round of which will take place in Baghdad on May 23, Israel and the United States have both warned military action remains an option should diplomacy fail.
Washington has sided with the UAE in the dispute over the Gulf islands of Abu Musa, Greater Tunb and Lesser Tunb.
More than 4,500 troops – 1,800 of them from France – took part in the military exercises, which were previously held in 1996, 2000, 2005 and 2008.
During the manoeuvres, troops simulated a war pitting the UAE and its ally against a neighbouring state which has invaded the Gulf country.
"We are able to work together (in the) air, land and sea and also have combined teams with Emirati and French officers and soldiers," Giller told reporters.
"It went very well."
France has bolstered its military ties with the Gulf state since it set up its first permanent military base in Abu Dhabi, the wealthiest and largest of the UAE's seven emirates.
The base, which hosts around 500 French army, navy and air force personnel, was opened by President Nicolas Sarkozy in 2009.
France is a leading military supplier to the UAE, and the two countries are linked by a 1995 defence pact.