Of the 31 PTI members, 29 submitted their resignations on the direction of their leader Khan who has said his party men will not sit in the assemblies which are the product of massive rigging.
Two members --Nighat Inqiar and Jahanzaib Kichi --defied the party's decision and did not submit their resignations.
The PML-N government would not be affected by the resignations as it has over 200 seats in the 272-member House.
The Pakistan People's Party (PPP) and PML-Q are the other opposition parties with six and seven seats respectively.
PTI members in the National Assembly submitted their resignations last week.
However, the party was yet to decide whether its members will resign from the Kyber Pakhtaunkhawa Assembly where it is in government.
Khan has said he would quit the Kyber Pakhtaunkhawa government after consulting his party allies.
The Speaker will not accept the resignations till talks between the federal government and protesters end, PML-N leader Rana Arshad told PTI.
The National Assembly Speaker has also not yet accepted the resignation submitted by PTI lawmakers.
"I will not demand the dissolution of the assemblies if Prime Minister Nawaz Sharif resigns till an independent investigation into the May 2013 rigging allegations is completed," Khan has said.
Political stalemate has continued for the last two weeks with Khan-led PTI and cleric Tahir-ul-Qadri's Pakistan Awami Tehreek (PAT) refusing to budge from their demand of the Prime Minister's resignation over allegations of rigging in last year's general election and killing of 14 PAT supporters in Lahore on June 17.