Dr Taj Hargey won substantial damages from the Muslim Weekly newspaper in a High Court libel case after it accused him of not being a true Muslim.
Dr Hargey, who previously backed a school's legal battle over its refusal to let a pupil wear the niqab in class, claimed the attack reflected tactics by the "Muslim Establishment" to smear those who question their authority.
In what is believed to be the first case of its kind in the UK, Dr Hargey sued and won a five-figure sum from the newspaper.
Dr Hargey said: "This historic case highlights the right to freedom and dissent within the British Muslim community and represents a crushing defeat for Muslim McCarthyism in this country.
"Just as US politicians terrorized the American electorate by unfairly labelling their foes as communists or communist sympathisers, the Muslim clergy uses the same intimadatory tactics to impose theological uniformity and cultural compliance in the community.
"Iconoclastic thinkers, liberals and non-conformists who dare to challenge this self-assumed religious authority in Islam by presenting a rational or alternative interpretation of their faith are invariably branded as apostates, heretics and non-believers."
Dr Hargey, chairman of the Muslim Educational Centre of Oxford (MECO), had brought proceedings in London's High Court against the publisher and editor-in-chief of The Muslim Weekly, a leading newspaper within the community.
His advocate, David Price, told Mr Justice Eady that the May 2006 article alleged that Dr Hargey held himself out as the chairman of MECO and a practising Muslim when he was a Qadiani and therefore a non-Muslim - a matter that he sought to conceal.
It also alleged that he was misleading the public by holding himself out as the chairman of a Muslim organisation and arranging events in that capacity, notwithstanding his true non-Muslim beliefs.
Mr Price said that it also claimed that Dr Hargey was sacked from his post teaching Islamic studies at the University of Cape Town as a result of the fact that he was a closet Qadiani.
He added that the truth was that Dr Hargey was not a Qadiani but had always been a devout and observant Muslim.
He spoke and lectured widely about Islam and had at no stage misled the public or represented himself as anything other than a committed mainstream Muslim.
In fact, Mr Price said, Dr Hargey was well known as a passionate believer of orthodox Sunni Islam and regularly appeared as a key representative of the Islamic faith in academia and the media, including regional and national television and radio programmes.
He was not dismissed from his post in Cape Town, where his academic responsibility was history and not Islamic studies, but left the university of his own accord at the end of his fixed-term appointment contract because he had been offered a better research position elsewhere which he chose to take up.
Afterwards, Dr Hargey said the settlement would also have significant repercussions for those calling for the imposition of Sharia law in Britain.
He said he has been a "thorn in the side of Muslim hierarchy" because he has openly endorsed non-niqab and non-beard-wearing Muslims, sanctioned marriages of Muslim women to men of other faiths, actively promoted mixed congregations in mosques, arranging for the first ever female-led Muslim congregational prayers to be held in the UK last October.
In 2007, he offered to help fund a school's legal battle over its refusal to let a pupil wear the niqab in class.
The settlement was revealed in a statement read out in the High Court. Muslim Media Ltd and Ahmed Malik have apologised and agreed to pay Dr Hargey substantial damages and his legal costs.