The 51-year-old Slovenian lawyer was the only candidate going forward for election at the UEFA Congress in Rome.
Ceferin took over two and a half years ago after the corruption scandal that toppled his predecessor, Frenchman Michel Platini.
"I am honoured," said Ceferin, thanking members of UEFA's 55 member associations for re-electing him, saying he was taking over with "fewer doubts and less scepticism than back then".
"The most dangerous thing we can do is rest on our laurels and bask in our current situation," he continued.
"So, what's going to happen now? That is the question many people were asking when I was elected two and a half years ago," said Ceferin.
"It was a legitimate and pertinent question. A question that I asked myself, to be totally honest with you. It was a bit of a jump into the unknown.
"At that time, football, at both world and European levels, was being rocked by the most serious governance crisis in its history and yet you decided to entrust the keys to the UEFA house to a virtual unknown."
Previously the head of the Slovenian Football Federation, Ceferin's presidency has so far been marked by his discretion and a less charismatic approach than that of Platini.
The Frenchman is still suspended until October this year, when he will complete a four-year ban from all football-related activities following the corruption scandal that also brought down then-FIFA chief Sepp Blatter.
Ceferin defended his record since taking over with his most notable achievement being the introduction of term limits for UEFA presidents, to a maximum of three four-year stints.
"Limited terms of office, the publication of salaries, the creation of a Compensation Committee and the inclusion of independent members in a reinforced Governance and Compliance Committee are just a few of the common-sense reforms we have introduced," he said.
"This is only the start. 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."
Ceferin promised to work closely with world football governing body FIFA.
"With our unity restored, we will be a source of constructive ideas for FIFA, rather than one of opposition. And we expect the same attitude from FIFA."
The UEFA chief also promised to work to bring the 2030 FIFA World Cup back to Europe.