In a shock ruling, a panel of judges said that Board of Control for Cricket in India (BCCI) president Anurag Thakur and the organisation's number two Ajay Shirke had to stand down immediately.
"The Supreme Court passes an order directing the BCCI president and secretary to desist from any board functions from hereon," said the ruling.
The order comes after judges also slapped restrictions on the BCCI's accounts last year over its failure to implement a series of reforms recommended by a panel headed by a former top judge, Rajendra Mal Lodha.
Cricket's massive popularity in India has helped the BCCI become by far the wealthiest of all of cricket's national boards, netting massive money from sponsorship and TV deals.
But it has also been embroiled in a series of scandals, including accusations of corruption and match-fixing that tarnished the Indian Premier League (IPL), the board's lucrative Twenty20 competition.
A corruption and match-fixing scandal in the sixth edition of the IPL in 2013 brought about the downfall of the board's president Narayanaswami Srinivasan after his son-in-law was accused of betting on matches.
Two of the eight franchises in the IPL were suspended as a result of the scandal, including the Chennai Super Kings which was owned by Srinivasan's India Cements company.
The elevation of Thakur and Shirke had been seen as representing a break with the past.
But the board's reluctance to implement Lodha's recommendations, which included age limits and term limits on office-bearers, had triggered a number of legal battles.
The recent series against England was nearly cancelled on the eve of the first Test as a result of the funding restrictions.
There was no immediate reaction from Thakur on Monday's announcement although Shirke appeared to accept the ruling.
"That is the Supreme Court's order and I cease to be secretary and that is absolutely fine. I have nothing to react because my role in BCCI is over," he said in brief comments to the NDTV network.
"If the Supreme Court has asked Anurag ji and me to leave the BCCI, that's fine, we'll leave the BCCI.
"I don't regret anything, I have no personal ambitions."
In his response to the latest judgement, Lodha said that it was an inevitable consequence of the board's foot-dragging.
"One should understand that when the order of the Supreme Court, which is the highest court of the land, has come, it has to be obeyed by all. It is the law of the land. Nobody can escape it," Lodha told reporters.
"There were obstructions. There were impediments. We fixed the timeline that was not adhered to. We submitted three reports before the Supreme Court, even then it was not implemented."
