Passing the court's ruling, Judge Silvino Pampino said there was insufficient evidence to convict Marcos of 32 counts of illegal money transfers abroad during the 20-year rule of her husband, Ferdinand.
"This court cannot in all conscience convict the accused on the basis of mere hearsay and on the basis of documents which were not authenticated and proved in the proper manner," he said in his judgment.
Pampino said the prosecution had failed to prove Marcos' wrongdoing beyond a reasonable doubt.
"The accused has the constitutional presumption of innocence."
Marcos, famous for her extravagant lifestyle and huge shoe collection, said she was "so happy and I thank the Lord that the 32 cases have been dismissed".
"This will subtract from the 901 cases that were filed against the Marcoses," she told local television.
During 20 years in power, the Marcoses, their relatives and business associates were accused of looting up to $10bn from state coffers.
Imelda Marcos herself was accused of spending state money to lavish herself with clothes and jewellery, responding to critics by saying that being beautiful was her "gift" to the Philippine nation.
Since the Marcoses were forced from power only about $1.8bn of the alleged missing billions has been recovered and many of the tycoons suspected of having benefited from ties with the family remain in control of their companies.
Ferdinand Marcos was ousted in an army-backed popular revolt in 1986 and died in exile in Hawaii in 1989.
Imelda Marcos returned to the Philippines in 1991 and was later allowed to bury her husband's remains in a refrigerated crypt in his home town of Batac.
She ran for the presidency in 1998 and lost.