The tumor "was removed" and Noriega was now lying in an intensive care ward at the Santo Tomas Hospital in Panama City, his daughter Thays Noriega told AFP.
Earlier she said the surgery "had to be done given that his quality of life was steadily diminishing."
Noriega's lawyer, Ezra Angel, said the operation was "successful," but did not have further details.
Manuel Noriega was a military intelligence officer who long worked for the CIA and who ruled his Central American country from 1983 until US forces invaded in 1989 to topple and capture him.
Relations between Noriega and the United States had deteriorated as he defied pressure from then US president Ronald Reagan to stand down, and as he appeared to shift allegiance to the then-Soviet Union, at the height of the Cold War.
After his ouster, Noriega was taken to the United States, where he was tried and imprisoned on drug trafficking and money laundering charges.
In 2010 Noriega was extradited to France, where he was convicted on money laundering charges, then extradited to Panama in 2011, where he was sentenced for the disappearance of political opponents during his reign.
The former dictator is currently serving three 20-year prison sentences in Panama for those rights abuses.
Temporary release
Noriega was being held in El Renacer prison, on the banks of the Panama Canal. But in January he was granted temporary release into home detention to prepare for the surgery, which had originally been scheduled for February.
Noriega had been suffering from a benign meningioma, a tumor on membranes that cover the brain and spinal cord just inside the skull.
The tumor had shown "unexpected growth," which boosted the need for surgery to avoid damage to the brain, his personal doctor, Eduardo Reyes said, adding that Noriega's age had meant he was a "high-risk patient."
The question now is whether Noriega will be returned to his cell after recovery.
His family has argued that given his age and frailty he should remain under house arrest. Noriega has suffered several strokes, lung complications, prostate cancer and depression, his relatives say.
But authorities have given no indication that he would avoid serving the rest of his prison sentence.
"Decisions on forms of detention rest with the courts, and that will never be unanimity there because there are scars that have never healed," a constitutional law expert, Miguel Antonio Bernal, told AFP.
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