Some 197 of the IAAF's 213 member federations were present for the vote.
In a Special Congress in Monaco, 182 member federations voted for the reforms, with 10 against and five invalid votes. Some 197 of the IAAF's 213 member federations were present for the vote, the result of which was a major boost for Coe.
"Let me thank you for the confidence that you have shown the Council today in the reform proposals that you have agreed to. This is a very important moment in the history of our sport," said Coe.
Coe's reforms, with a nod to disgraced predecessor Lamine Diack's abuse of the presidency, include stripping himself of some powers, with the president and IAAF Council not allowed to serve more than 12 years and with more checks put in place.
"Too much power rested in the hands of too few people," Coe said.
The reforms also push for gender balance, handing athletes a greater voice and crucially establishing an independent integrity unit that would manage all anti-doping matters and be responsible for greater intelligence gathering.
"We're putting in place a framework that should have been there years ago," Coe said, telling members that they should all feel "violated" given the amount of money that had been siphoned off instead of having been "used for the development of athletics."
"It's bad enough that any of this happened, but it cannot happen for a second time, not on our watch, not anyone else's watch.
"Let's not beat around the bush, our sport, our family, is under threat. Sitting out the fight is not an option."
Since Coe took office in August 2015, the IAAF has been mired in the fall-out from the presidency of Diack, at the centre of a corruption scandal in which several former senior IAAF officials were found to have bribed Russian athletes in return for keeping quiet over positive doping tests.
Coe admitted that the reforms had not been to everyone's taste, all the while praising the "civilised discourse" and the "clarity and honesty of dialogue".
"The fundamental principles, I believe, have broad support," said the Briton, a two-time Olympic 1500m gold medallist.
"On gender balance, a number of areas told me they needed more time - you've got it.
"I want checks and balances in place... I don't want to be in an office choosing carpets and signing off expenses.
"I would not ask for change if I didn't think we needed it."
Coe's bold stance on gender equality envisages the 26-member Council transitioning to half-men, half-women by 2023. At the 2019 Council election, he wants a minimum of nine of each gender elected including two vice-presidents of each gender.
Indicative of the ground shift that will entail was that just three of the representatives of the 42 member federations who addressed the Congress before the vote were women, notably women's world marathon record holder Paula Radcliffe representing Britain and also including representatives from the Cook Islands and the Turks and Caicos.
"We have to put these changes in," said Radcliffe. "There is only one choice, there isn't time to delay and talk about this, we need to act now to save our sport."
Notably voting against the reforms was Saudi Arabia while Qatar, the host of the 2019 World Athletics Championships and 2022 Football World Cup, voted for.
Abstainers included Lamine Diack's Senegal, vice-president Sergey Bubka's Ukraine and track powerhouses Jamaica, despite Usain Bolt picking up a record sixth IAAF Athlete of the Year award on Friday and throwing his weight behind Coe.
"I know that Seb Coe is trying to make track and field more transparent to everyone so they can see what shape it is in and to make sure there is not one person fully in control," said Bolt.
"That's a bold move from him as IAAF president.
"That's also helped the sport to make people more confident and to trust the sport more."