The four-member appeals bench led by Chief Justice Surendra Kumar Sinha gave the order on Monday after hearing leave-to-appeal petitions by the State.
The top court also ordered Manna to surrender his passport before he is released from jail.
On Feb 24 last year, Gulshan police started a case charging Manna for inciting a military takeover after two audio clips of Manna's telephone conversations with BNP leader Sadeque Hossain Khoka and another unidentified man were leaked.
They were heard discussing plans to engineer clashes at Dhaka University and incite the army to destabilise the government. Manna was arrested the next day.
On Mar 5 the same year, police started another case accusing him of sedition.
Manna moved the High Court after he was denied bail in the trial court.
On Aug 30 this year, he secured bail in the sedition case.
The State moved against it and got a two-month stay on the order, but was told to file a leave-to-appeal petition.
In the case of inciting the army, the High Court on Nov 10 granted bail to Manna.
The State also challenged it and secured a stay until Nov 27. It was then also instructed to a file a leave-to-appeal petition.
The Supreme Court gave its decision on Monday after hearing the pleas the previous day.