The court said there was “no justification” to keep him in custody for any longer.
Mr Zubair, the co-founder of the fact-check website Alt News, was arrested last month by Delhi police over a 2018 tweet, purportedly a screenshot of a scene from a 1983 Bollywood classic Kissi Se Na Kehna.
But he was charged over his fact-checking work in Uttar Pradesh, the state headed by Hindu monk-turned-politician Yogi Adityanath.
A bench led by Justice DY Chandrachud said there was no justification to keep Mr Zubair in detention, as the allegations by police in the northern state were the same as by those in Delhi.
“Having regard to the fact that the petitioner has been subjected to a comprehensive investigation by the Delhi police, we find no reason for his deprivation of personal liberty to persist,” the bench said.
The bench ordered the transfer of all cases against him to Delhi and instructed the Special Investigation Team formed by Mr Adityanath’s government to be disbanded.
The court ordered Mr Zubair’s release on interim bail by presenting a bail bond of 20,000 rupees ($250) before the magistrate court at Delhi’s Patiala House.
Mr Zubair had already received bail in one of the cases from the apex court, and was separately given relief by a Delhi court in the lone case in the capital city.
Mr Zubair was first arrested by Delhi police after an anonymous Twitter user said he was “hurting religious sentiments” over a 2018 tweet that contained a screenshot of a classic Bollywood film showing “Honeymoon Hotel" repainted as “Hanuman Hotel” – the Hindu monkey god.
The image accompanied Mr Zubair’s comments: "Before 2014: Honeymoon Hotel, After 2014: Hanuman Hotel", a perceived reference to the rise in Hindu extremism since Prime Minister Narendra Modi’s BJP came to power in 2014.