Opposition leaders say that the ban violates Venezuela's constitution, which upholds the political rights of all citizens unless they have been charged with a crime and sentenced by a court.
None of those on the list have been formally sentenced.
"At this moment, in Venezuela, there is a list of hundreds of Venezuelans that are being discriminated against," Leopoldo Lopez, a dsiqualified candidate for mayor of Caracas, said.
"We are marching with the constitution in hand and the support of the people."
More than one dozen members of the 1999 assembly that drafted the current constitution, including Chavez's ex-wife Marisabel Rodriguez, have accused Russian of violating the law.
The comptroller general is "illegally excluding those who don't share the president's socialist agenda," she said during Saturday's march.
"I am feeling the abuses that the people feel. I feel them as part of the population. It hurts me, here I am on the side of the people."
Chavez has rejected claims that he ordered the potential candidates to be barred from running.
"No, they are not my orders," he told a rally on Friday rally.
Chavez said that the protesters "should be ashamed of themselves'' for defending candidates suspected of corruption.
Opinion polls indicate the opposition - which currently controls two states - could take about 10 of the 23 state governor posts up for grabs in November.