Coe, who won four Olympic medals, including two golds, as a middle distance runner, headed London's successful bid to host the 2012 Olympic Games.
A former lawmaker, he became a life member -- known as a lord -- in the upper house of Britain's parliament in 2000.
confirmed that Coe, previously a vice-president, had become their sixth president at the 50th IAAF Congress in Beijing on Wednesday, beating rival and former Ukrainian Olympic pole vaulter Sergey Bubka in the final vote.
"I am deeply honoured that our sport has placed its trust in me. There is no job I want to do more -- nor with greater commitment," Coe was quoted on the IAAF website as saying.
Coe's appointment comes at a turbulent time for the athletics body, as it battles doping allegations.
Earlier this month, Britain's Sunday Times and German broadcaster ARD revealed they had access to a leaked database containing more than 12,000 blood tests from 5,000 athletes from 2001 to 2012. Leading experts concluded that these that these revealed an "extraordinary level of cheating" in the sport.
However the IAAF denies athletics is suffering a similar crisis to professional cycling's culture of doping when the sport was bedeviled by extensive drug-taking and accusations of top-level coverups in the 1990s and 2000s.
"If transparency is an issue, we would welcome any investigation from the only authorized body to investigate -- the World Anti-Doping Agency (WADA)," the IAAF's anti-doping manager, Thomas Capdevielle, told CNN.
Meanwhile, Coe called the reports "sensationalizing" and an attempt to "destroy the reputation of the athletes and our sport." He told the Associated Press that it was a "declaration of war."
But Australian doping experts Michael Ashenden and Robin Parisotto, who analyzed the leaked tests, concluded that endurance events from the 800 meters to the marathon had produced "suspicious" results.
At the major competitions, this equated to nearly 150 medalists, including 55 champions.
The IAAF has published a lengthy statement denying any wrongdoing, one that was accompanied by a detailed nine-page rebuttal of the allegations.
"What the IAAF cannot accept under any circumstances ... is an accusation that it has breached its primary duty to act in the best interests of the sport of athletics," the statement read.
But Hajo Seppelt, an investigative journalist who has spent much of his working life scrutinizing the world of doping, remained unrepentant.
"I am used to this kind of reaction because I have been working on doping stories for almost 20 years. Always, when I present facts about failures, this is the normal reaction," the German told CNN. "The 'declaration of war' statement is ridiculous. We are not interested in blaming sport. They should react to facts."
Coe will take office on August 31, after the IAAF World Championships in China's capital.