Boban voiced his “total disapproval” of a proposed amendment to the organisation’s statutes that would ensure Aleksander Ceferin could stay in power for another seven years, accusing the Slovenian of pursuing his “personal aspirations” at the expense of morality and ethics.
The resignation comes barely two days after Ceferin broke his public silence on a growing row triggered by the planned rule change in an exclusive interview with Telegraph Sport.
Boban said in a statement: “It is with sorrow, and a heavy heart, I have no option but to leave Uefa.
“I am not trying to be some sort of hero, especially as I am not alone in my thinking here.
“Despite having expressed my deepest concern and total disapproval, the Uefa president does not consider there to be any legal issues with the proposed changes, let alone any moral or ethical ones, and he intends to move forward regardless in pursuit of his personal aspirations.”
Details of the row over Ceferin’s plans were made public after a meeting of Uefa’s executive committee in Hamburg during last month’s draw for this summer’s European Championship.
A proposal was made to amend statutes that currently limit terms of office for executives – including a president – to 12 years.
Ceferin himself introduced the measure in response to the 2015 Fifa scandal which brought down his predecessor, Michel Platini.
There is a disagreement over whether those rules were intended to apply to terms that began before they first came into force in 2017 – Ceferin was first elected the previous year.
The proposed amendment would end any debate about whether the Slovenian would be able to stand for re-election in 2027 and serve as president for 15 years.
David Gill, the Uefa treasurer and former Manchester United chief executive, told the Hamburg meeting he opposed a change that could also allow him personally to remain in office for 20 years.
Gill and others believe he and Ceferin should be setting an example by standing down early.
Boban praised Ceferin for having backed reforms early in his presidency but said “his shift away from these values is beyond comprehension”.
“I fully appreciate that nothing is ideal, let alone myself, and at times compromises may be necessary,” Boban wrote. “However, being party to this would go against all the principles and values I wholeheartedly believe in and stand for.”
Boban’s departure is the most public show of growing discontent with Ceferin’s leadership since the Slovenian lawyer was re-elected unopposed in April.
Uefa publicly thanked Luis Rubiales, its disgraced former vice-president, for his service when he resigned for forcibly kissing Jenni Hermoso when Spain won last year’s Women’s World Cup.
It then tried to bring Russia’s youth teams back into European competitions despite the country’s ongoing invasion of Ukraine – a move Ceferin told Telegraph Sport he wanted to resurrect.
Ceferin also denied the proposed change on term limits was an attempt to extend his own mandate, claiming it was to rectify an invalid provision that had never been properly approved by Uefa’s member associations.
He added: “This is a matter of fact, not a legal issue. I have not yet decided whether I want to run for office again or not. To be honest, I am very tired.”
Ceferin speculated he could end up serving a partial third term so he did not stay longer than 12 years.
But when asked if he would commit to that, he replied: “I don’t commit to anything. Not to run. Not to not run. Let’s wait.”
In response to Boban’s departure, Uefa said: “Uefa extends its gratitude to Mr Boban for his dedicated service and wishes him the best of luck in his future career endeavours.”