Egyptians lined up Saturday to pick the first president since the ouster of Hosni Mubarak, choosing between a standard-bearer of the old secular autocracy and a veteran of its Islamist opposition, even as a power grab by Egypt’s ruling generals ended the hope that the vote would complete Egypt’s transition to democracy.

The runoff election this weekend was to have been the culmination of a nearly 18-month transition since the 18-day uprising that forced out Mr. Mubarak, the moment that the generals who seized control after his ouster said they were waiting for to hand power to an elected civilian, inaugurate a new democracy, and end six decades of military rule.

Instead, the vote took place in the shadow of the generals’ moves just a day before to shut down the democratically elected, Islamist-led Parliament, take over lawmaking authority and vow to issue their own interim constitution, which would define the role of the leader voters were choosing on Saturday.

“This is the end stage of the whole transition,” said Mahmoud Ismail, 27, a political activist in the town of Menoufia. “To be or not to be.”

The actions by the ruling military council on Friday, acting on a court ruling rushed out on the eve of the vote that dissolved Parliament, foreclosed the possibility that the Islamists of the Muslim Brotherhood might immediately take control of both the Parliament and the presidency. And it raised the likelihood that the new president will be either wrestling the military for power in a longer political struggle or perhaps collaborating and doing its bidding.

Many called it a soft coup, and some voters said they had all but abandoned their hopes for the man they would elect. “The president who is coming will have no powers whatsoever,” said Mohamed Saqr, 51, a bank manager waiting to cast his vote in the working class Cairo neighborhood of Saeda Zeinab.

The two candidates, meanwhile, representing the main opposing forces of the Mubarak era, pushed ahead with their campaigns, mobilizing their respective battle-tested political machines.

The Islamist, Mohamed Morsi of the Muslim Brotherhood, waited in line to cast his vote in the Nile Delta town of Zagazig where he used to teach engineering. “God is great,” a throng cried as he emerged. He saluted those killed demonstrating against Mr. Mubarak. “Today is the day of the martyrs,” he declared. “There is no place at all for Mubarak’s helpers.”

The other candidate, Ahmed Shafik, a former Air Force general and Mr. Mubarak’s last prime minister, cast his ballot in the style of his former boss. Surrounded by a heavy guard of military and police officers, he visited a school-turned-polling place in an upscale suburb. The lines were pushed aside and guards immediately closed the facility for his private use.

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