The Pakistan election commission announced on its website that Iftikhar Uddin won Chitral's only seat in the national assembly and Haji Ghulam Muhammad gained its sole seat in the provincial assembly of Khyber Pakhtunkhwa.
Both contested on behalf of the All Pakistan League Party (APML), which Musharraf founded in exile before he returned home and was put under house arrest, barred from contesting the elections in person.
He faces the possibility of going on trial for treason and is wanted in three other cases dating back to his 1999-2008 rule.
The former leader took power in a coup that deposed then prime minister Nawaz Sharif, now set to return to power after winning a commanding victory in the polls.
The APML announced on May 3 that it was boycotting the election, but its candidates in Chitral refused to pull out.
APML official Muhammad Amjad welcomed the wins.
"It proves the love of people for Musharraf," Amjad said.
Musharraf had applied to contest four seats for the national assembly, including one from Chitral, but was barred from standing by the courts over charges of conspiracy to murder and violating the constitution.
Amjad said that Uddin inherited the party ticket in Chitral as a result.
Syeda Afshan Adil, one of Musharraf's lawyers, told AFP that party leaders in Chitral protested against the boycott on the grounds that the retired general is popular in the mountain region, partly for building a key tunnel that has eased travel.
Musharraf returned to Pakistan in March after four years of self-imposed exile, promising to "save" the country from militancy and economic collapse.
But he is now under house arrest over the murder of opposition leader Benazir Bhutto in 2007 and for sacking judges in the same year, during which he imposed emergency rule.
In addition he faces a third legal case over the 2006 death of a Baluch rebel leader and has been threatened with death by the Taliban.