The 78-year-old head of state’s surgery lasted just over five hours at the University of Tokyo Hospital.
The emperor, who has suffered from poor health in recent months, plays a largely ceremonial role but is respected deeply by many Japanese.
He ascended the throne in 1989 following the death of his father, Emperor Hirohito.
Emperor Akihito was accompanied by his wife Empress Michiko when he checked into the hospital on Friday morning.
The operation began at around 09:30 (00:30) on Saturday and ended at around 15:30.
“The operation went smoothly as planned,” one of the three surgeons, Minoru Ono, told a news conference. “We confirmed a sufficient blood flow back in the arteries.”
The emperor had reportedly nodded and told his wife and daughter “it feels good” as he emerged from the effects of the anaesthetics.
But another surgeon, Atsushi Amano, said it was too early to talk confidently of the operation’s success, saying it would be “measured by whether the emperor can regain the normal lifestyle he had wished for”.