CAIRO - Egyptians lined up Saturday to pick their first president since Hosni Mubarak even as a last-minute grab for power by the ruling generals called the whole exercise into doubt, raising questions about whether the vote would be the long-promised culmination of Egypt’s transition to democracy or an empty gesture amid the reconstitution of a military-backed autocracy.

Voters faced a stark choice between two faces of the past: Ahmed Shafiq, a former air force general and Mubarak stalwart who promised to restore order and thwart the rise of an Islamist theocracy, or Mohamed Morsi, a veteran of the once-outlawed Muslim Brotherhood campaigning as a defender of the revolution against a return of the old order.

The ruling military council that took power after Mubarak’s ouster 16 months ago had pledged that this weekend’s two-day presidential runoff would be the final step in the transition to civilian government, the moment they would hand power to the first democratically elected leader in Egypt’s long history.

But the day before the vote, the generals shut down the democratically elected and Islamist-led Parliament, acting on a ruling rushed out by a court of Mubarak-appointed judges. They declared they would be the sole lawmakers, even after a new president is elected. And they began drawing up a new interim constitution that would define the power of the president whom voters were choosing 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 generals’ moves abruptly changed the stakes in the presidential race.

If Morsi wins, he will face a prolonged struggle for power against the generals, while Shafiq - who for at least a decade had been considered Mubarak’s likely successor - could emerge as a new military-backed strongman unrestrained by either a constitution or Parliament.

Shafiq, Mubarak’s last prime minister, has made no public comment on the dissolution of Parliament. He cast his ballot Saturday in the style of his former boss, arriving at a polling place in an upscale suburb surrounded by a heavy guard of military and police officers. The lines were pushed aside and guards immediately closed the facility for his private use.

Crowds of his supporters were waiting both inside and outside the polling place. “The Brotherhood is dissolved,’’ they chanted, cheering at the dissolution of the Brotherhood-led Parliament. State media reported that a cameraman in a military vehicle filmed Shafiq’s trip to the ballot box, apparently to preserve it for posterity.

Morsi of the Muslim Brotherhood has cast the election as the last chance to beat back the full return of the Mubarak autocracy. He waited in line in the nearly 100 degree heat Saturday to cast his vote in the Nile Delta town of Zagazig, where he used to teach engineering. “God is great,’’ a throng of supporters cried as he emerged, and he shouted over them to salute those killed demonstrating against Mubarak.

“Today is the day of the martyrs,’’ he declared. “There is no place at all for Mubarak’s helpers.’’

Each candidate revved up a battle-tested political machine. Morsi turned to the Brotherhood’s system of local cells and charities built over 84 years of preaching and politics. Shafiq, who surged to roughly tie Morsi in the first round of voting, scarcely a month after he announced his campaign, relied instead on the network of local power brokers who had made up Mubarak’s defunct ruling party.

In Shafiq’s campaign offices in Menoufia, in the Delta province, operatives of the old ruling party said Saturday that they were enjoying the fun of Egypt’s first competitive presidential race. “This is a good feeling, if you don’t know what will happen,’’ said Tarek al-Warraqui, a campaign staffer who previously worked as a press officer for the local government. “Before, we know.’’

He mocked the Brotherhood’s missteps and bragged about his colleagues’ proficiency in the bare-knuckle politics of the district.

“We have a network,’’ he said. “We have someone in every village. The Brotherhood’s experience is different,’’ he said. “We worked in the light. They were underground.’’

He displayed fliers he had printed and distributed throughout the district calling the Brotherhood members liars, associating them with US officials, and, improbably, portraying them as disgraced members of the former government.

It was an extension of a campaign of bold inversions that Shafiq himself has leveled against the group. In reality, many of the Brotherhood’s leaders endured jail sentences and some of its activists were tortured because of their opposition to Mubarak’s rule. During last year’s revolt, its cadres were a mainstay of the protests in Tahrir Square.

But after entering the runoff against the Brotherhood’s candidate, Shafiq began accusing the group of complicity in the Mubarak government. He said that bearded Islamist gunmen tied to the Brotherhood were responsible for shooting demonstrators in Tahrir Square, and his supporters even filed murder charges against Brotherhood leaders to drive home the point.

In a television interview two nights ago, Shafiq, who sometimes says he still admires Mubarak, even claimed credit for Mubarak’s ouster.

“I’m the one who proposed the idea of stepping down, and I proposed it insistently,’’ he said. He had proposed it in a meeting with the top military leader, field marshal Mohamed Hussein Tantawi and former vice president Omar Suleiman to plot a response to the uprising, he said, and it took “perseverance’’ to persuade Tantawi to carry it out.

Playing off the signs that the military-led government was determined to hold back their ascent to power, Brotherhood leaders held several news conferences to accuse Shafiq and his supporters of various schemes of electoral fraud.