“ Egypt could see ‘dangerous’ days ahead if power returned to those linked to the previous regime,” it said.
The group's candidate, Mohammed Mursi, faces ex-PM Ahmed Shafiq in a runoff presidential election this weekend.
The court said last year's parliamentary vote - the first free and fair poll in decades - was unconstitutional, and called for fresh elections.
The decision effectively puts legislative power into the hands of the ruling Supreme Council of Armed Forces (Scaf), who were tasked with overseeing Egypt's transition after the toppling of President Hosni Mubarak in February 2011.
The court also upheld the right of Mr Shafiq to run for president.
Some Brotherhood activists express hope that the situation can be turned to their advantage amid public suspicion that the ruling Supreme Council of Armed Forces and remnants of the former government are trying to stay in power.
Yet many analysts believe that the court decisions now make a win for Mr Shafiq even more likely. The former air forces commander is widely seen as the unofficial candidate of the generals who took power after President Mubarak was forced from office in February 2011.
Whichever man wins will inherit a difficult security situation, a struggling economy and a nation that now seems bitterly divided.
Activists, who fear Scaf is trying to increase its power, have denounced Thursday's rulings as a "coup" designed to undermine the revolution, carried out by judges appointed under former President Mubarak.
The BBC's Jon Leyne in Cairo says that while judges were expected to rule that some parts of the parliamentary poll was illegitimate, the court went much further by ordering a complete re-run.