The top Democrat at the city Board of Elections’ Brooklyn office was suspended without pay Thursday — the second head to roll amid a probe into the mysterious purge of more than 126,000 Democratic voters from the borough rolls.

Brooklyn Deputy Chief Clerk Betty Ann Canizio-Aqiil, 68, was suspended from her $120,000-a-year job, BOE Executive Director Michael Ryan announced.

Last month, the board suspended Brooklyn Chief Clerk Diane Haslett-Rudiano, a Republican, from her $125,000-a-year position over the April 19 presidential primary fiasco.

The board had come under criticism for disciplining the Republican clerk last month and not the Democratic one, even though the vast majority of purged voters were Brooklyn Democrats.

Democratic presidential candidate Bernie Sanders called New York City’s voter disenfranchisement a national disgrace.

Ryan defended the belated action.

“We want to make sure that when we take full and final action, it’s done based on all the facts and done appropriately,” he said.

There were 121,056 city residents who voted by affidavit ballot because their names were not on the voter rolls.