The power-sharing unity government was brokered by US Secretary of State John Kerry following the disputed 2014 presidential elections, but has since been weakened by infighting between rivals.
Parliament removed the transportation and education ministers on Sunday, citing poor performance and bringing the total number of ministers dismissed to five over two days.
Finance minister Eklil Hakimi was the only minister on Sunday to survive the vote, a relief for international donors and the government.
The vote took place despite pleas from Afghan President Ashraf Ghani and Chief Executive Abdullah Abdullah to halt further action against the cabinet.
"President Ghani and Dr. Abdullah told MPs that their decision will deal a huge political blow to the government at this critical time and urged them to stop the process," Mirdad Najrabi, chairman of parliament's security commission, told Reuters.
A statement released by Ghani's office said the government did not want confrontation and respected the decision of the parliament, but asked the House of Representatives to suspend its decision.
Parliament, which has a constitutional right to sack ministers, may hold votes on as many as 11 more ministers.
"This is our right and we will use it and will not let the government politicize this process," lawmaker Gul Padsha Majidi said before Sunday's vote.
Parliament on Saturday dismissed three ministers including Foreign Minister Salahuddin Rabbani.
The deteriorating political situation in Afghanistan could become a major foreign policy challenge for US President-elect Donald Trump, who has said little about Afghanistan on the campaign trail.
Kabul was supposed to have overseen fresh parliamentary elections and a constitutional grand council to re-establish political legitimacy.
However, a two-year deadline has passed with none of the promised steps taken, leaving question marks over the future of the government at a time when political uncertainty is already being stoked by rising ethnic tensions.