The pardon, part of a seasonal amnesty, will reduce her 33-year jail sentence by six years.
Former president Win Myint, who was ousted along with Ms Suu Kyi, also received a reduced jail sentence after getting two of his charges pardoned.
Periodic amnesties have been announced before, but this is the first time they have included Ms Suu Kyi and Mr Myint.
Last week, Ms Suu Kyi was moved from prison to house arrest in the capital Nay Pyi Taw.
The 78-year-old Nobel laureate has been detained by the military since February 2021 following the coup that ousted her.
The coup triggered civil war in the country, and has led to the deaths of thousands of people.
The military junta has also been accused of unleashing disproportionate violence against those opposing its rule.
Some countries, notably China and Thailand, have started a dialogue with the junta, but these initiatives have been criticised for excluding Ms Suu Kyi’s party, which won a huge majority in 2020 elections.
The extent of the win led the military to allege election fraud – which they then used as a justification for the coup.
Any negotiations on a compromise with the opposition would almost certainly require the involvement of Ms Suu Kyi. She has, however, been kept isolated since her arrest. Almost no news has emerged about her condition for more than two years.
Ms Suu Kyi is appealing against the convictions on the other offences, which range from election fraud to corruption.
All the charges – which she has denied – were brought against her in closed-door, military-run trials. Rights groups have condemned the court trials as a sham.
The military junta on Monday postponed an election it had promised would be held by August this year.
