The Pakistan Tehreek-e-Insaf (PTI) chief received 176 votes during the election for 22nd prime minister of the country against PML-N president Shehbaz Sharif's 96 votes during the National Assembly session today.
Mr Khan is to be sworn in as Prime Minister on Saturday.
Khan is assured to win, following his party's victory in last month's general elections.
The key decision of the major reshuffle was taken in a high-level meeting headed by PTI chairman Imran Khan and attended by Jahangir Tareen, Shah Mehmood Qureshi and former Khyber Pakhtunkhwa chief secretary Arbab Shehzad.
The Pakistan People's Party (PPP), the third largest party in the house that joined the PML-N and others in an opposition alliance, withdrew its support for Shehbaz Sharif's candidature as Premier days before the election and abstained from voting, Dawn online reported.
Death of Vajpayee end of an era, says Prime Minister Modi
Vajpayee, 93, passed away at the All India Institute of Medical Sciences (AIIMS) here last evening after a prolonged illness. From there it would be taken to the BJP headquarters tomorrow, where people would be able to pay their last respects.
A former Member of Parliament from the Bhartiya Janta Party, the 54-year-old also expressed grief on the demise of former Indian Prime Minister Atal Bihari Vajpayee.
Khan's PTI won the July 25 election, but did not have enough seats for an outright majority, forcing its leader to partner with smaller parties and independents in order to form a government.
Rival parties have alleged "blatant" vote-rigging.
Khan and the PTI campaigned on promises to end widespread graft while building an "Islamic welfare state". "It will be good for the subcontinent also", Khan said.