Salafist politician Hazem Abu Ismail, considered a key candidate along with the two, is also among the total of 10 candidates barred from running in the elections.
Farouk Sultan, the head of the Supreme Presidential Election Commission, on Saturday confirmed the decision, but declined to give any details on the reasons for their disqualification.
Suleiman, a former ally of Mubarak whose nomination had sparked protests, was apparently barred because he failed to get enough signatures to endorse his last minute candidature, BBC reported.
The hardline Islamists hopeful Abu Ismail was ruled out because his mother has American citizenship. Shater, the leader of the powerful Muslim Brotherhood, has been barred because of a former criminal conviction.
The candidates and their supporters have expressed anger over the move and large demonstrations are expected in the capital, the report said. Candidates who have been disqualified can appeal the decision within 48 hours.
First round of elections is due in May, more than a year after former President Hosni Mubarak was ousted. Candidates who remain in the race include former Arab League chief Amr Moussa, moderate Islamist Abdul-Moneim Abulfotouh and former prime minister Ahmed Shafiq.