The May 1999 Time cover story "Suharto Inc" alleged Suharto and his family had amassed billions of dollars during his presidency, including more than $9bn stashed in Swiss bank accounts.
The Suharto family had originally sought damages from time equivalent to $19.5bn when it first filed the lawsuit in 1999.
A lawyer for the former president welcomed what he called a "surprise verdict".
The case was originally thrown out by the Jakarta district court in June 2000.
Suharto then lodged an appeal with a higher court, which was turned down in March 2001.
Monday's supreme court's ruling was passed by a panel of three judges, including a retired general who rose in the military ranks under the Suharto presidency.
Born June 8, 1921
Served as general in Indonesian army
Seized power from Indonesia's first president Sukarno in 1965
Established 'New Order' government characterised by strong central government and repression of dissent
Forced to resign in 1998 amid widespread protests triggered by Asian financial crisis
Suharto was forced to resign from the presidency in 1998 as riots and pro-democracy protests swept Indonesia in the wake of the Asian financial crisis.
In its ruling the supreme court said Time would also have to publish apologies in its various editions, as well as several local newspapers and magazines.
Suharto, a former general, seized power following a 1965 coup the exact circumstances of which remain unclear.
In the following 32 years he ruled Indonesia with an iron fist and is accused of killing or imprisoning hundreds of thousands of political opponents.
Too ill for trial
Monday's court ruling is likely to spark outrage among Indonesian critics who allege the Suharto family was engaged in massive corruption during his presidency.
|Suharto's son Tommy was recently |
questioned by prosecutors [Reuters]
Suharto and his family have always denied the allegations.
The former ruler has successfully fought off all attempts to date to charge him with embezzlement after his lawyers argued he was too ill to stand trial.
He currently faces a lawsuit filed by the attorney general that seeks to retrieve $1.54bn in alleged stolen state funds.
Last month Suharto's youngest son Tommy wsa questioned by prosecutors over a multi-million dollar graft case involving the state clove monopoly that he chaired until it was disovled in 1998.
Tommy Suharto was freed from jail in 2005 after serving four years of a 15 year sentence for ordering the murder of a judge who had convicted him of corruption and illegal possession of weapons.
A spokesman for Time in New York told the Associated Press that the magazine had no comment on Monday's verdict since it had not received any notification from the court about a ruling.
He said the magazine continued to stand by its story.
Time is owned by Time Inc., the magazine publishing division of media conglomerate Time Warner Inc.
The magazine has said the article was based on four months of reporting in 11 countries that uncovered a network of corporate investments, bank transfers and property holdings in Switzerland, Uzbekistan and Nigeria.
The report alleged that Suharto and his children amassed $73 billion, the bulk from lucrative contracts and concessions in oil, mining, forestry, property, banking and petrochemicals.
It said much of that wealth was lost during the 1997 Asian financial crisis, but the family still had $15bn when Suharto stood down in 1999.