The former head of the Slovenian Football Federation was the only candidate in the poll of the organisation's 55 members and will serve for four years.
"I am honoured," said Ceferin. "The most dangerous thing we can do is rest on our laurels and bask in our current situation."
Ceferin took over in 2016 from Michel Platini, who was ousted after becoming submerged in a wave of corruption scandals
"At that time, football, at both world and European levels, was being rocked by the most serious governance crisis in its history," Ceferin recalled. "And yet you decided to entrust the keys to the Uefa house to a virtual unknown."
Since becoming the European game's most powerful administrator, the former lawyer has reduced the influence of Uefa presidents. They can now serve a maximum of three four-year stints.
He has also shaken up the organisation's committees to ensure greater independence and more credibility.
"This is only the start," he added. "We will be doing more in this area because there remain weaknesses in our system.
"When crisis hits, it is not the time to suddenly forsake everything that has gone before. I am not the president of a 'new Uefa'. I am the president of Uefa, a Uefa that can be proud of its past and confident about the future."