Musharraf's All Pakistan Muslim League (APML) won one seat each for National Assembly and Khyber Pakhtunkhwa's provincial assembly from Chitral's NA-32 and PK-90 constituency.
The APML had announced a boycott of the general elections 2013 after the rejection of Musharraf's nomination papers from all provinces and the imposition of a lifetime ban.
However, some of the party candidates had decided to stay in the field despite the boycott.
Iftikhar ud Din won the NA-32 seat with 19,938 votes, defeating his nearest rival from the Tehrik-i-Insaf Pakistan led by Imran Khan.
Ghulam Mohammad, APML candidate from PK-90, won his seat securing 10,646 against Pakistan Peoples Party candidate who had received 10,524 votes.
In PK-89 constituency, the Pakistan People's Party's Saleem Khan with 11,285 votes defeated APML's Shehzada Khalid.
Musharraf, 69, currently is under house arrest on judicial remand at his Chak Shehzad residence, which was declared as a sub-jail, after a bench of the Islamabad High Court rejected the extension of his bail in the 2007 judges detention case.
Musharraf returned to Pakistan on March 23 after more than four years in self-exile to participate in the upcoming elections.