Fujimori is currently in prison in Chile fighting extradition to Peru over charges of human rights abuses and corruption.
The election board forbid him from running in April's presidential elections, as expected, citing a congressional ban on his holding public office until February 2011.
A legal notice published in El Peruano newspaper said: "Citizen Alberto Fujimori Fujimori is subject to special disqualification."
Congresswoman Martha Chavez, a staunch Fujimori supporter, registered her candidacy late on Monday hours before a midnight deadline, along with Santiago Fujimori, the former president's brother, as her first vice-president.
Fujimori arrived unexpectedly in Chile in November following five years in exile in Tokyo, where he flew in 2000 when his decade-long autocratic regime collapsed.
His daughter Keiko registered his candidacy on Friday, hours after the Chilean judge handling his extradition ordered him to remain under arrest, possibly for months, while the case is processed.