Musharraf has also been arrested over the imposition of emergency rule in 2007, the assassination of former premier Benazir Bhutto and the killing of Baloch leader Akbar Bugti in a 2006 military operation.
Muhammad Amjad, the spokesman for Musharraf's All Pakistan Muslim League (APML), announced their party's boycott of the polls at a news conference in Islamabad.
"The rejection of Gen. (retd) Pervez Musharraf's nomination papers has resulted in this decision by the party," he said.
"Musharraf will face all cases against him and will not run away from any charges," Amjad said.
All 170 candidates fielded by the APML had withdrawn from the polls, Amjad said.
The 69-year-old former president has been humiliated since he returned to Pakistan from self-exile in March to contest elections.
He is now being held in his farmhouse, which was declared a sub-jail after his arrest.
On Tuesday, the Peshawar high court banned Musharraf from contesting elections for the rest of his life.
APML officials told media that they believe free and fair polls are not possible under the current Election Commission.