Mr. Morsi’s victory is an ambiguous milestone in Egypt’s promised transition to democracy after the ouster 16 months ago of President Hosni Mubarak. After an election that international monitors called credible, the military-led government has recognized an electoral victory by an opponent of military rule over Mr. Shafik, who promised harmony with the Supreme Council of the Armed Forces.

But Mr. Morsi’s recognition as president does little to resolve the larger standoff between the generals and the Brotherhood over the balance of power over the institutions of government and the future constitution. Under the generals’ plan, Mr. Morsi, 60, will assume an office stripped of almost all authority under a military-issued interim constitution…

In Tahrir Square, at least, the confirmation of Mr. Morsi’s win is expected to bring celebrations instead of clashes. His designation as president-elect will hand the Brotherhood and its allies a bully pulpit to use the struggle for power with the military. The Brotherhood has sought to rebuild the partnership with more secular and liberal advocates of democracy that came together in the uprising against Mr. Mubarak, and Brotherhood leaders have vowed not to hold any negotiations with the generals without the participation of the other groups in their so-called “national front.”