This was despite numerous credible eyewitness accounts that the demolition, which took just a few hours, had been rehearsed and carried out with impunity and the connivance of a section of the local police in front of thousands of spectators.
Last year, India's Supreme Court conceded it had been a "calculated act" and an "egregious violation of the rule of law".
So how do we explain the acquittals?
Generally the verdict is being seen as another indictment of India's sluggish and chaotic criminal justice system. Many fear it has been damaged beyond repair by decades of brazen political interference, underfunding and weak capacity.
But more specifically the verdict has thrown into sharp relief the increasing marginalisation of India's 200 million Muslims.
Under Narendra Modi's Hindu nationalist BJP government, the community has been pushed into a corner and feels more humiliated than at any time in the history of pluralist, secular India, hailed as the world's largest democracy since independence in 1947.
Mobs have lynched Muslims for eating beef or transporting cows, which are sacred to majority Hindus. Mr Modi's government has amended laws to fast track non-Muslim refugees from neighbouring countries. It has split the Muslim-majority state of Jammu and Kashmir and stripped it of its constitutional autonomy.
This year, Muslims were singled out and blamed for spreading the novel coronavirus after members of an Islamic group attended a religious gathering in Delhi. Larger Hindu religious gatherings during the pandemic received no such political, public or media opprobrium or scape-goating.
That's not all. Muslim students and activists have been picked up and thrown into prison for allegedly instigating riots over a controversial citizenship law in Delhi last winter, while many Hindu instigators went scot-free. The Babri verdict, many Muslims say, is just a continuation of this humiliation.
The sense of alienation is real. Mr Modi's party makes no bones about its Hindu majoritarian ideology. Popular news networks openly demonise Muslims. Many of India's once-powerful regional parties, which once stood by the community, appear to have abandoned them. The main opposition Congress is accused by critics of using Muslims cynically to harvest votes without providing much in return. The community itself has few leaders to speak up for it.
"Muslims are simply losing faith in the system. They feel cornered and feel the political parties, institutions and the media are failing them. There is a lot of despondency in the community," says Asim Ali, a research associate at the Centre for Policy Research, a Delhi-based think tank.
Demonstrators in Delhi, India, protesting against the citizenship law.
In truth, India has a long history of marginalising Muslims. They "carry a double burden of being labelled as 'anti-national' and as being 'appeased' at the same time", according to one report. But the irony is that, while many Indians have bought the Hindu nationalist bogey that Muslims are being unfairly rewarded, the community has not in fact benefitted from major socio-economic gains, say historians.
Muslims are disproportionately squeezed into ghettos in India's teeming cities. Their share in India's elite federal police officers force was below 3% in 2016, while Muslims make up more than 14% of the population. Only 8% of India's urban Muslims had jobs which paid a regular salary, less than double the national average, one report found.
Enrolment of children at primary school levels was high, but so were dropouts at high school, largely because of economic deprivation. Muslim representation in India's parliament have been declining consistently - below 5% in the elected lower house now, down from 9% in 1980. When the BJP swept to power in 2014, it was the first time a winning party did so without a single Muslim MP.
Mr Modi and his colleagues have consistently said their party doesn't discriminate against any religion. The prime minister has said he enjoys the support of many Islamic nations and his expansive welfare benefits reach every poor Indian, irrespective of religion or caste. For years, the BJP has described the liberal opposition parties as "pseudo secular".
Some believe there is truth in this allegation. As an example they point to the Communists who ruled West Bengal state in eastern India for more than three decades and were avowedly secular, ensuring the protection and security of Muslims, who form nearly a quarter of the state's population.
Yet, studies revealed that Muslims in Gujarat, a state marked by religious tension and sectarian politics, fared economically better and in human development indices than their counterparts in Bengal. "The market place is non religious in India. So in states like Gujarat where business thrives both Hindus and Muslims do well," says Mirza Asmer Beg, a professor of international relations, at Aligarh Muslim University.
But analysts say religious electoral competition practised by the BJP has led to the "otherisation" of Muslims. "How do you polarise? By making the other a threat to your identity," says political scientist Christophe Jaffrelot. He believes India is moving towards an "ethnic democracy", born out of ethnic nationalisation which implies a "strong sense of belonging and of superiority".
It's not all dark yet. There is the rise of a young and articulate middle class unencumbered by the ghosts of partition. The widespread protests against the citizenship law saw a large number of these articulate Muslim men and women taking to India's streets and breaking stereotypes of a cloistered and voiceless minority. Community coaching classes have sprung up, training young Muslims to prepare for India's prestigious and competitive civil service exams. "Many of the young Muslims do wear their identity on their sleeves in a positive way and are not afraid to voice their views," says Mr Ali.
But, in the end, the acquittals will only deepen anxieties and a sense of injustice among India's Muslims. "In many ways, it is an abandoned community. There's a feeling of powerlessness. Muslims have been exploited by both their own and Hindu leaders and all parties for years," says Zaheer Ali, a political scientist. "Poverty has made things worse."
Also read: Indian court acquits top BJP leaders in Babri mosque case