The South Asian island has been locked in political gridlock for over a month since President Maithripala Sirisena replaced former Prime Minister Ranil Wickremesinghe with Rajapaksa, who was then twice sacked by parliament but has refused to resign.
Foreign countries have yet to recognise the new government.
Friday's motion, which passed 122 to none in the 225-member parliament, followed a similar vote on Thursday to cut the budget to the Prime Minister's office. Rajapaksa loyalists also skipped that vote, arguing the motion was illegal.
"The motion to cut down the expenditures of ministers, deputy ministers, and state ministers is passed," parliament's speaker Karu Jayasuriya said. He earlier said he would officially inform ministry secretaries of the decision.
The motion specifically was to prohibit top civil servants from paying out salaries and travel expenses.
However, one senior civil servant from a government ministry, speaking to Reuters on condition of anonymity, said it was unclear how such a vote would be applied in practice because there were questions over whether due process had been followed.
In a repeat of Thursday's actions, Rajapaksa loyalists denounced the vote and called into question the impartiality of the speaker.
"The motion presented today is illegal and we have mentioned it to the speaker too. We will not attend such illegal motions," Anura Priyadharshana Yapa, a minister in Rajapaksa's disputed government, told reporters before the proceedings started.
Later, Rajapaksa and Wickremesinghe met in the parliament, sources close to the two men told Reuters.
"They spoke about the way forward," one source said, adding that the impasse was unlikely to break before a court ruling on whether President Sirisena's Nov. 9 decision to dissolve parliament was constitutional.
That verdict is expected on Dec. 7.
Separately on Friday, the Appeal Court began a hearing on a petition signed by 122 legislators that challenged Rajapaksa's authority to hold office after he lost two no confidence votes earlier this month.
Rajapaksa's party argues that its government should remain in power because the president never accepted the no confidence votes.
The motions presented on Thursday and Friday are based on the assumption Rajapaksa has been sacked, thus he deems them illegal.
Rajapaksa presided over a government victory over Tamil rebels in 2009, ending a bloody 26-year civil war. (Reporting by Ranga Sirilal and Shihar Aneez Writing by John Geddie; Editing by Nick Macfie and Darren Schuettler)
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