They want the disgraced former president to repay almost $US2 billion in stolen funds and damages.
It revives efforts to retrieve some of the many billions in state funds thought to have been siphoned-off by Suharto and his family during 32 years in power.
As Radio Australia's finance and business correspondent Karon Snowdon reports, it is a case that might result in some justice, even though it will be largely symbolic.
The case, filed in the South Jakarta District Court on Monday, is going after more than $US400 million prosecutors allege was directly stolen, and just over $US1 billion dollars in damages.
A former human rights and anti-corruption commissioner, HS Dillon, has witnessed all previous failures to prosecute through three successive presidents.
"In Javanese culture you are not supposed to attack or malign your elders so they can pass their old age in peace," he said.
"[Post-Suharto president BJ] Habibie would have never brought Suharto to there.
"[Abdurrahman Wahid, popularly known as] Gus Dur did, and I was there when he did that, he had actually proposed that according to Islamic law if he could give some of his money back there would be Islah - as the Arabs say, there would be some sort of resolution to this.
"With [Megawati Sukarnoputri, or] Mega, she did not go against him, because... they didn't want to create precedence that one day will go against them."
While a civil case goes some way to improve the Yudhoyono government's credibility in going after the corrupt, Suharto's human rights abuses during his three decades in power finally go beyond the current government's interest.
Suggestions that Suharto's billions all in the family
It is alleged Suharto funnelled the money to his family's companies through the Supersemar Scholarship Foundation, which he chaired.
Some of the companies belonged to his son, Tommy.
HS Dillon says the case is not so much about punishing Suharto, 86, but more about finally establishing a case for prosecuting the dictator's children.
It is thought they have many billions of ill-gotten dollars stashed in overseas accounts.
"The real thinking at that time and we were working with Gus Dur Abdurrahman Wahid and Marzuki Darusman, the [then-]attorney-general, the strategy was to prosecute, then to convict Suharto, and then eventually to pardon him," he said.
"The main objective being once he had been convicted, even though he had been pardoned, then we would have been able to get to his children and to his cronies.
"There would have then been a sense of 'justice has been served'.
"[But] I don't think any Indonesian really would like to see this old president of theirs behind bars, but they would like to see the children.
"So if this really goes well - which is a really big if - then what we could see is that his wealth is in his children's names and all that.
"If that can be shown to be coming through him then that could be confiscated [and] would be a partial sense of justice, if the ill-gotten wealth could be returned to the public."
But as the failure of successive attempts to prosecute Suharto has shown, there generally seems to be little effort in snaring the dictator.
"I think [this time] it's pretty serious because this chap who is now the attorney-general, he is a very serious guy."
HS Dillon says the main factor arresting Indonesia's development is a culture of impunity, both against corruption and human rights violations.
To circumvent this, the current attorney-general, Hendarman Supandji, has brought a civil case as it does not require Suharto's appearance in court.
Previous criminal charges have failed when doctors have claimed Suharto's poor health made him unfit to stand trial.
More at www.radioaustralia.net.au/connectasia