Ahmed Jadallah / Reuters Supporters of the Muslim Brotherhood's presidential candidate, Mohamed Morsy, celebrate his victory in Cairo's Tahrir Square on June 24, 2012

The decision took an excruciatingly long time to announce. Not only had the original schedule been pushed back a couple of days for declaring a winner in Egypt’s first democratic presidential election. But when the Supreme Presidential Election Commission (SPEC) finally came out to meet the press and present its findings on Sunday, its chairman went on a virtual filibuster about calumnies against his group, swinging from perceived bias to pointillist detail about electoral minutiae as the entire country awaited the verdict. Finally — almost grudgingly — the SPEC certified that Mohamed Morsy of the Islamist Freedom and Justice Party, the political organization of the Muslim Brotherhood, had been elected President by 51.73% to 48.27% for Ahmed Shafik, the former Prime Minister under deposed President Hosni Mubarak who was the other contender in the runoff.

Filling Cairo’s immense Tahrir Square with its supporters, the Brotherhood celebrated the news. It is, in its way, a stunning turnaround in Egyptian history. Long banned by the Mubarak regime, the Brotherhood had tenaciously hung on to its influence, fielding “independent” candidates in whatever elections in the political space allowed by the regime. It is, however, a limited victory.

(MORE: Morsy Wins Egyptian Presidency, but Will the Military Cede Any Power?)

Before the votes could actually be counted in last weekend’s election, the Supreme Council of the Armed Forces (SCAF) — the junta that has effectively ruled the country since Mubarak’s fall last February — announced measures that made it clear it was in charge, no matter who filled the presidency. Indeed, it will oversee the process in which the country’s new constitution will be written — a critical component of Egyptian democracy. Almost in tandem, Egypt’s Supreme Constitutional Court dissolved the Brotherhood-dominated parliament and gave the military the right to run the country with martial law powers until the new constitution is written.

The junta might well have exercised its muscle and insinuated Shafik, a former air-force commander, into the presidential suite. But Morsy’s numbers — attested by a number of observers as well as the Brotherhood’s tradition of scrupulousness in its own vote count — may have been difficult to suppress. Besides, there is much to be gained from dealing with the Brotherhood. The Islamist organization may have been the victim of the regime and the military’s hostility in the past, but it has learned to bend in order to move ahead politically. That pliancy — as well as the appearance of democratic fairness in having an opposition force win — could buy SCAF more time to forge the kind of Egypt that will preserve the military’s prerogatives and status in society.

(PHOTOS: Egypt’s Presidential Runoff Brings Out Both Voters and Protesters)

Indeed, much of the time the country spent waiting for the winner may have been an opportunity for SCAF and the Brotherhood to negotiate a modus vivendi. While Morsy, a Ph.D. graduate in materials science from the University of Southern California, will not have the kind of authoritarian powers that Mubarak wielded, he will still possess enough to make a mark in social reforms. Certainly, many Egyptian secularists fear what the Brotherhood might do to what remains of nonsectarianism in the country. The country’s large Coptic Christian minority, in particular, is said to be particularly fearful of an Islamist ascendancy. SCAF has already said, however, that it will retain the right to decide on all matters regarding the military, including whether or not to go to war. It is also unlikely to allow the Morsy Administration to control the Ministry of the Interior, which is in charge of internal security in the country and has had a reputation of thuggery dating back to the Mubarak regime.

As Cairo correspondent Abigail Hauslohner and writer Tony Karon said in the latest issue of TIME, the junta “is clearly in charge, despite the Brotherhood’s political heft. SCAF may have run the show from backstage for months, but it is now openly claiming the authority to change the rules of the game on a whim — including the … President’s term in office.” The Brotherhood will thus likely play along, further isolating the secular sectors of Egyptian society, who may try to rouse the public again in the name of the so-called revolution of February 2011. No matter, write Hauslohner and Karon, “the junta won’t feel threatened by a few thousand protesters in Tahrir.”

PHOTOS: Egypt in Flux: Photographs by Yuri Kozyrev