Egypt’s final presidential race will be between the Muslim Brotherhood’s candidate, Mohammed Morsi of the Brotherhood’s Freedom and Justice party, and a former air force general Ahmed Shafiq, a law and order candidate and Mubarak’s last Prime Minister, despite complaints about irregularities and vote-rigging in the first round.Morsi received 5.7m votes (24.3% of those cast), followed by Shafiq with 5.5m (23.3%). Hamdeen Sabbahi, the independent Nasserist, got 4.8m (20.4%), Abdel Moneim Abul Fotouh, an independent Islamist, 4m (17.2%) and the former Arab League chief Amr Moussa 2.5m (10.9%). Abul Fotouh was the only candidate to reject the results outright.

For all the talk of polarisation, nearly half of the first-round votes went to candidates in the middle ground. Turnout was 46% of some 50 million registered voters.

Of all the likely outcomes of the first round of the two-stage contest, this is the most polarised, pitting the long-banned Brotherhood – the world’s oldest Islamist movement – against a secular figure who is seen as a remnant of the old regime.

For many supporters of the revolution that saw Mubarak deposed after 30 years in February 2011, this was a ‘nightmare’ outcome to the first election for an Egyptian leader in which the outcome was not known in advance.

Supporters of losing candidates hoped that complaints about irregularities including vote-rigging would produce a different final result. But the electoral commission rejected all appeals after re-checking vote counts.

Moussa, who had been seen as the front-running ‘stability’ candidate, said on Monday that he would back neither of the presidential finalists, rejecting both a ‘religious state’ and a state ‘run by remnants of the former regime’.

Sabbahi’s Karama party has said it will boycott the runoff on 16 and 17 June. ‘The party rejects the notion of the Muslim Brotherhood dominating the country’s legislative bodies. And it also rejects the notion of handing power over to remnants of the old [Mubarak] regime.’

Hani Shukrallah, veteran commentator of Egypt’s most widely circulated newspaper, al-Ahram, wrote: ‘Having stunned themselves and the world by staging a great revolution, at enormous sacrifice, many Egyptians felt they were back to square one, the very square which their despised deposed president used to taunt them for 30 years: ‘It’s me or the Muslim Brotherhood.” But he added: ‘It’s not a new dawn of the Muslim Brotherhood we are witnessing, nor a revival of the police state, but the twilight of both.’

Dr Solava Ibrahim, of Manchester University, UK, said that ‘many will choose to abstain from voting in the runoff. No matter what the results of the elections will be, it is clear the Egyptian revolution still has a long way to go until it achieves true power.’