The vote paves the way for Mr Aleman to face charges of embezzlement and money laundering.
"
The (National) Assembly is sending a message that nobody is
above the law
"
Congress member Walmaro Gutierrez
Reports from the capital Managua say supporters of Mr Aleman demonstrated outside the headquarters of his party after the vote, burning tyres in the streets before police moved in to restore order.
Judge Ileana Perez, who has opened a fraud investigation into Mr Aleman, has ordered him to be available for questioning as early as Friday afternoon, the AFP news agency reported.
"The arrest warrant was issued immediately," said Nicaragua's acting attorney general Francisco Fiallos.
Mr Aleman is alleged to have diverted around $100m in public funds to banks in Panama - a sum equal to the government budget for a whole year.
Anti-corruption pledge
He is also accused of misspending $1.3m in public funds that were destined for state-controlled television but never arrived there.
He denies any wrongdoing.
Mr Aleman served as president from 1997 until January of this year when his deputy, Enrique Bolanos, took over pledging to clean up the country's corrupt government.
Mr Bolanos made a televised speech late on Thursday, saying he hoped Mr Aleman received a fair trial.
The motion to strip him of his immunity was passed after members of Mr Aleman's governing party joined the opposition in a 47-45 vote.
"The (National) Assembly is sending a message that nobody is above the law," Congress member Walmaro Gutierrez said after the vote.
The BBC's Nick Miles says the case has galvanised public opinion across all sectors of Nicaraguan society.
A recent poll suggested that up to 90% of Nicaraguans supported putting Mr Aleman on trial.
The accusations against Mr Aleman first emerged eight months ago.
In September, he was removed as head of Congress after half a million people had signed a petition urging his immunity from prosecution be lifted.