Sanjaasuren Oyun, the leader of the minority Civil Will Party and a member of parliament, told AFP that parliament debated well into the night before ratifying Wednesday's mass resignation, a move that will lead to Elbegdorj's dismissal after less than two years in power.
All 10 cabinet members belonging to the Mongolian People's Revolutionary Party (MPRP), which has dominated politics for most of the nation's 14 years of post-Soviet democracy, triggered the crisis when they resigned on Friday.
Hundreds of angry protesters took to the streets of the capital, Ulan Bator, on Thursday in support of the prime minister, although the situation had eased on Friday after the deployment of police and security forces.
With the MPRP holding exactly half of the 76 seats in parliament approval of the resignation - and the fall of Elbegdorj's government - was almost a foregone conclusion.
All 76 delegates were present and 39 voted for while 37 abstained.
The decision to topple the government "has immediately created a dangerous situation in our country", Elbegdorj, who belongs to the Democratic Party, told AFP without elaborating.
"I think this is a short-sighted wrong move of the Mongolian Communists"
Mongolian Prime Minister
"I think this is a short-sighted wrong move of the Mongolian Communists. It could also be a desperate action of some of the party executives to cover up their misdeeds, unlawful acts when my commitment to root out corruption in public offices started threatening their interests."
A spokesman for the MPRP's youth organisation however said it was good for Mongolia.
The spokesman, who declined to be named, said: "It will lift the confusion that has been existing regarding the government. It will be clearer who should take primary responsibility for government policies."
The MPRP is expected to promote one of its own as the next prime minister.
Oyun said: "Parliament will reconvene either on Wednesday or Thursday when possibly a new government will be formed."
Constitutionally, the parties are supposed to engage in negotiations in the coming days to form a new government and the MPRP will try to attract some of the small parties into a new coalition.
Oyun said her party would not co-operate with the MPRP.
"I don't think they will completely change the policies. Probably they will go slower on corruption efforts. In 2000 to 2004 they did very little on corruption."