The lawsuit against Suharto alleged corruption in the setting up and running of the tax-free foundation he established, ostensibly for charitable purposes.
State-owned companies and other large businesses, foreign and local, were obliged to contribute to the foundation.
Judge Wahyono said prosecutors were unable to prove the amount of immaterial damages they were demanding, but said the foundation had stolen state funds by siphoning money to companies linked to the dictator.
Wahyono, who like many Indonesians goes by a single name, ruled that Suharto could not be personally responsible because the decisions were made by the foundation board, not him.
He said it was "fair and fitting" that Supersemar return $110 million to the state, around 25 per cent of the figure alleged to be missing in the lawsuit.
Ordering the foundation to return any more would hamper its ongoing charitable work, he said.
Suharto died in January without facing criminal prosecution over allegations that he oversaw massive corruption during his more than three-decade rule that benefited his family and cronies.
Suharto's family and their associates are believed to have amassed billions of dollars during Suharto's 32-year rule, according to anti-corruption group Transparency International.
The civil suit against Suharto began last year as part of a revived effort
|Suharto's death in January left a mixed legacy|
as some see him as a hero [GALLO/GETTY]
by the current government to bring him to justice.
A criminal suit against him was abandoned in 2006 on health grounds.
Suharto's son, Hutomo "Tommy" Mandala Putra Suharto and his five
siblings came to control some of Indonesia's largest conglomerates
during Suharto's 32-year rule.
The children are alleged to have used their connections to secure contracts and demand kickbacks.
There was no immediate response from Suharto's children, who were not in court to hear the verdict.
If Suharto had been found guilty, any damages would have been paid from his estate.
In previous hearings, prosecutors told the court that during the 1980s and 1990s, the Supersemar foundation paid money to companies owned by members of the Suharto family or their close associates.These included a privately owned bank, an airline controlled by one of Suharto's sons, a logging firm, and a cooperative linked to Golkar, the political party which was run by Suharto and which is now a member of the ruling coalition.