Malik told reporters at the airport in Karachi that he had submitted his resignation to the Chairman of the Senate or upper house of Parliament.
On Jun 4, the apex court suspended Malik's membership of the Senate on the ground that he had failed to provide proof of renouncing his British citizenship.
The court has suspended the membership of nine members of the national and provincial assemblies in response to petitions filed against lawmakers with dual nationality.
Malik described his move as a "personal decision" aimed at countering the impression that a bill moved in Parliament today to allow persons with dual nationality to contest polls would primarily benefit him.
"I will do whatever the party wants...I gave up my dual nationality in 2008 and now I have resigned from the Senate because I do not want anyone maligning me," he said.
He contended his resignation was a "sacrifice" for 1.2 million Pakistanis with dual nationality getting the right to vote.
Malik said the Parliament should be allowed to decide the issue of dual nationality.
He further rejected reports that he had extensive business interests in Britain and said all firms he had established while living in self-exile had been "made redundant".
At the time the apex court suspended Malik's membership of parliament, he was the Interior Minister.
He was subsequently appointed the Special Advisor to the Prime Minister on Interior Affairs so that he could continue heading the Interior Ministry.