Zardari used his “discretionary powers” to pardon Malik, said presidential spokesperson Farhatullah Babar.
“Rehman Malik has all along maintained that he has been victimised due to political reasons in his absence from the country,” Babar said.
Malik, one of Zardari’s key allies in his ruling Pakistan People’s Party (PPP), was sentenced while abroad to three years’ imprisonment by an anti-corruption court in January 2004.
Under Pakistan’s National Reconciliation Ordinance, passed by military ruler Pervez Musharraf in 2007, political opponents were allowed to return to the country without fear of possible court proceedings.
However, the supreme court overruled the ordinance last December, ordering hundreds of cases to be re-opened and millions of misappropriated dollars to be returned to the state.
Meanwhile a bomb planted on a bicycle killed 12 people in north-west Pakistan on Tuesday.
Another ten people were injured when the bomb was detonated remotely as a senior police officer drove through the outskirts of the city of Dera Ismail Khan in North-West Frontier Province.
The Pakistani Taliban, Tehreek-e-Taliban Pakistan, has claimed responsibility for the attack.