One young Cairo woman outside the court expressed the frustration felt by many protesters. "SCAF has been suppressing our protests, suppressing the youth movements on the ground, they have been arresting thousands of us," she said, referring to the Supreme Council of the Armed Forces.
But Amre Moussa, who was a foreign minister under Mubarak, was chief of the Arab League, and most recently a presidential candidate, played down the impact of the ruling on parliament.
"It is not a political move or a decision by the SCAF, it is a legal matter that has been referred to the tribunal, by individuals, by other parties," he told CNN's Christiane Amanpour.
As for the wrangling over who will write the new constitution, Moussa said it is not of crucial importance.
"The current constitutional declaration is enough to give the president the powers he needs," he said. "I believe that the president, once elected, knows exactly the powers he will use."
Following the court decision, Egypt's interim military rulers declared full legislative authority, creating anxiety and uncertainty about the country's future.
It was just on January 23 -- two days before the anniversary of the birth of a revolution that eventually toppled Mubarak -- when the military surrendered legislative powers to the first parliament in the country's history to be dominated by Islamists, whose two parties won about 70% of the seats in the lower house.
The military is considered by many to be a bulwark against the power and influence of Islamists in Egypt.
And some who fear the Muslim Brotherhood has gained too much strength may welcome this knock to the confidence built from its successes in the parliamentary vote.
"With parliamentary elections, there was this sense that the Brotherhood could now go for broke," Cook said. "They seem to have been outmaneuvered by the military and courts and associated supporters of the old regime. It may be time to make a deal to preserve themselves to fight longer."
All eyes will be on the conduct and outcome of the runoff this weekend.
Taken together, the military leadership's actions indicate "there's a high likelihood of Shafik being aided to victory by the military," Trager said.
But Khaled Fahmy, a professor at American University in Cairo, told Amanpour that people are "very confused" and split over who to back.
"Ahmed Shafik made a very powerful speech today, he tried to calm many people," he said. "But there is a lot of sympathy I think now for the Muslim Brotherhood -- there's a lot of fear of what Shafik is capable of doing.
"And because things now have become so clear and the gloves are off, people see what the military is intent on doing. Yesterday's ruling by the minister of justice giving the military police these excessive rights, this is a serious militarization of Egyptian society, that we made the revolution against."
Fahmy said he believes blunders by the Muslim Brotherhood are partly to blame for its current weakened position.
The Brotherhood has failed to get results in parliament, where its lawmakers have been "cocky" toward liberal forces, he said, and also failed to realize just how deep the military's influence runs through Egypt's intelligence and security services -- the so-called deep state.
The "legal coup" pulled off by the military is just the latest front in a long-running battle for dominance between the two sides, he said.
"This has been in the offing for not only months, but for years and years," Fahmy said.
"The events of today and indeed the past few weeks have shown very clearly the determination by SCAF to oust the Muslim Brotherhood altogether, and to deny it serious victories that it had won legitimately through by ballot boxes -- and today is the culmination of that struggle."