Women will be allowed to lead prayers at Taj Hargey's "Open Mosque" in Cape Town.
"We are opening the mosque for open-minded people, not closed-minded people," Mr Hargey told the BBC.
He says the mosque will help counter growing Islamic radicalism.
Mr Hargey, a professor at the Muslim Educational Centre of Oxford in the UK, told the BBC's Newsday programme it was time for a "religious revolution".
"In South Africa 20 years ago, there was a peaceful revolution changing from apartheid to democracy and we need to have a similar development in the area of religion," he said.
Mr Hargey, who was born in Cape Town, said the mosque would welcome people from all genders, religions and sexual orientations.
As well as leading prayers, women would also be allowed to pray in the same room as men, he said.
He contrasted this to the current Islamic practice which sees "women at the back of the street, back of the hall, out of sight, out of mind".
However, members of Cape Town's large Muslim community have taken to social media to criticise the new mosque, with some labelling him a "heretic" or "non-believer".
One group tried to block the opening of the mosque.
South Africa's umbrella body for Islamic groups, the Muslim Judicial Council (MJC), says it is investigating the new mosque and has noted concerns raised by the community.
But Mr Hargey insists that the idea of the Open Mosque does not go against Islam.
"The mosque we are doing is a replica of the original mosque of the Prophet Muhammad, where there were no barriers," he said.
"This idea of female invisibility is an innovation that came after Muhammad, unfortunately it has become entrenched."
