The 54-year-old decided to leave his post following a poor start to the final round of 2010 World Cup Qualifying which saw UAE lose their first two games against North Korea and Saudi Arabia earlier this month.
Former Senegal coach Metsu guided the UAE to the Gulf Cup title in January 2007 after taking over in June 2006.
"UAE Football Association accepted the resignation of coach Metsu from his post as the coach of the national team," said UAE FA president Mohammed Khalfan Al Romaithy on Monday.
"I would like to thank coach Bruno who had good success with the national team in the previous two years. He won the 18th Gulf Cup and led the national team to the 2007 Asian Cup finals and the final round of the 2010 FIFA World Cup qualifiers.
"There is an end to every job and life will not stop with the departure of coach Metsu. We will continue our aims to develop and support the national team especially as there are a lot of important commitments that we have."
Following the Gulf Cup triumph in 2007, Metsu's UAE failed to qualify from the group stage of the Asian Cup before finishing second in the third round of Asian World Cup Qualifying behind Iran to secure a place in the final stage.
"I would like to thank His Highness Khalifa bin Zayed bin Sultan Al Nahyan; UAE president and His Highness Mohammed bin Rashid Al Maktoum; UAE prime minister and Sheikh Mohammed bin Zayed Al Nahyan; Abu Dhabi Crown Prince," said Metsu.
"I also want to thank UAE FA president and all the officials for all the support that they gave to me. The technical staff that I worked with also helped me a lot and I want to thank the players for their help."
UAE will look to kickstart their bid for a place at the 2010 World Cup in South Africa against South Korea on October 15.