No fewer than 70 people originally filed applications to the Isie, which is organising the first presidential election since the January 2011 revolt forced Ben Ali to flee.
"Of the 70, 27 complied with all of the conditions and were accepted, while 41 were rejected," Isie chairman Chafik Sarsar told a news conference, adding that two other candidates withdrew.
The approved candidates include incumbent Moncef Marzouki, former premier Beji Caid Essebsi and National Constituent Assembly chief Mustapha Ben Jaafar.
The polls, along with parliamentary elections in October, are seen as a milestone in Tunisia's transition after more than two decades under Ben Ali.
The north African nation has in recent years grappled with social unrest over poor living conditions, violence blamed on hardline Islamists and attacks by militant groups including Al-Qaeda loyalists.
Marzouki was elected president in late 2011 by assembly members under a coalition deal with the moderate Islamist Ennahda party.
Other candidates running in the November election include Kamel Morjane, Ben Ali's last foreign minister, as well as another former minister under the dictator, Mondher Zenaidi.
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Also in the race are magistrate Kannou Kalthoum, former central bank governor Mustapha Kamel Ennabli and party leaders and businessmen.
Sarsar also said the prosecution service had been asked to open an investigation into allegations of possible fraud in voter sponsorship lists submitted by some presidential candidates.
"We cannot name names and we have no concrete evidence of such fraud. It will be up to the courts to decide," he said.
The Isie said that 1,327 groups were putting up candidates for the October 26 parliamentary election -- 1,230 in Tunisia and 97 abroad.
On September 23, Ennahda unveiled an ambitious platform for the parliamentary election, saying it is confident of a greater victory than the one achieved three years ago.
Ennahda headed a coalition until it stepped down in favour of a caretaker cabinet of technocrats earlier this year to bring an end to months of crisis sparked by the assassination of two leading opposition figures by radical Islamists.
Ennahda has indicated it will not field a presidential candidate, but will back a "consensus" hopeful.