The guilty verdict was considered ripe for appeal from the moment it was issued, because the judge who handed it down said at the time that he had seen no evidence to back up a conviction. Instead, the judge reasoned that Mr. Mubarak and his Interior Ministry bore responsibility for the deaths of the protesters by virtue of their positions; he acquitted a half-dozen subordinate Interior Ministry officials who were charged in the same case.

Under Egyptian law, the ruling on Sunday effectively rewinds the court proceedings to the original indictment of Mr. Mubarak in 2011. When the case is assigned to a new court, the judge will have broad latitude and can send the case back to prosecutors for further investigation and new evidence, or even amend the charges.

Evidently anticipating Sunday’s ruling, Egyptian prosecutors recently had begun a new case against Mr. Mubarak, accusing him of taking payoffs from the state news organization Al Ahram in the form of $1 million in gifts over the last six years of his rule. The prosecutors issued an order on Saturday that would allow them to go on detaining Mr. Mubarak for questioning in that matter even if the court threw out his conviction in the protesters’ deaths.

But on Sunday, the state media reported that Mr. Mubarak and his family had unexpectedly agreed to repay $3 million in gifts he and they had received from Al Ahram in order to resolve the charges. If the repayment is accepted, the judge who hears the retrial could decide whether Mr. Mubarak remains in prison or goes free in the interim.

On the other side, lawyers with Mr. Morsi’s Freedom and Justice Party and other advocates of a stronger conviction said they hoped that in a retrial, the prosecutors would take advantage of the findings of a presidential fact-finding commission looking into the protesters’ deaths.

The commission’s findings have not been disclosed publicly, but they reportedly include evidence that Mr. Mubarak was fully aware of the brutal tactics his police were using against protesters, something he denied in the first trial. Members of the commission have said that Mr. Mubarak received “firsthand” reports and watched the street battles around Tahrir Square on a video monitor in his office as they happened.

Ali al-Gineidy, a former member of the commission, said in an interview that Habib el-Adly, Mr. Mubarak’s interior minister, told the panel that “Mubarak knew everything, big and small.” Mr. Adly did not testify in the first trial, and it was unclear whether he would in the second.