The pair spoke for more than half an hour late on Saturday, said a foreign ministry spokesman.
Musharraf, on the cabinet's recommendations on Thursday, allowed clemency for Abd al-Qadir Khan, the father of Pakistan's nuclear bomb, after he confessed to passing nuclear secrets to Iran, Libya and North Korea and begged the nation's forgiveness.
While details of the talk were not immediately available, the News daily said Powell conveyed US President George Bush's concern about the role of Pakistani scientists in the nuclear proliferation to Iran, Libya and North Korea.
Musharraf assured him no such activity would be allowed in the future, it said. He said an effective National Command and Control Authority was in place and measures had been taken to prevent proliferation in future, the paper said.
"The conversation was very cordial and Powell understood Pakistan's point of view on nuclear scientists. He appreciated the way Musharraf handled the crisis"
The Nation daily
"The conversation was very cordial and Powell understood Pakistan's point of view on nuclear scientists," another daily, The Nation, said, quoting a government official. "Powell appreciated the way Musharraf handled the crisis," it added.
Powell on Friday stressed the clemency for Khan was a domestic question for Musharraf, who has emerged as a key US ally since 11 September 2001.
"This is a matter between Mr Khan, who is a Pakistani citizen, and his government. But it is a matter also that I'll be talking to President Musharraf about," Powell told reporters at UN headquarters in New York.
The top US diplomat said "goal number one" was making sure no more sensitive nuclear details were passed on by any Pakistani scientist, including Khan - dubbed by Powell the "biggest" of all nuclear proliferators.
"I'm pleased that President Musharraf realised that he had to do something about this network"
US secretary of state
"I'm pleased that President Musharraf realised that he had to do something about this network."
Musharraf said Khan was a hero for bringing the nuclear bomb to Pakistan, seen as a vital part of the national defences against nuclear-armed rival India, and granted him a pardon.
Musharraf said Khan had made "mistakes" and he had decided to pardon him because of his services to enhancing national security.