Staff at the newspaper, until April known as The New Age, were told they should not come to work on Sunday as the paper would be closed with immediate effect.
While staff would not be working in July, they were promised they would be paid their salaries.
Last night Manyi would not respond to calls on text messages on the closure of the newspaper.
The newspaper was first published in 2010 by the Guptas, backing the administration of former president Jacob Zuma who was closely linked to the family.
The New Age had signed a lucrative sponsorship deal with Transnet and the SABC to broadcast its breakfasts - a parliamentary ad-hoc inquiry found these only benefited the Guptas.
Manyi bought the media assets of the Guptas, The New Age newspaper and ANN7 news channel, in a vendor financing deal. In essence the Guptas lent Manyi’s Lodidox R450million to buy the assets.
Earlier this year MultiChoice announced ANN7 - now AfroWorld View - would from August not be broadcast on its DStv platform. This after the #GuptaLeak e-mails revealed MultiChoice paid the Guptas R25m before the channel had gone to air, and had increased its annual carriage fees to the channel from R50m to R141m. Staff were called to a meeting with Manyi yesterday and told the business wasn't doing well and would be shut down.