While the election was decided by secret ballot,the rebels secured at least five Coalition votes in a rebuff to the government made possible by a Labor ploy to nominate Mr O'Brien,one of Mr Joyce's closest allies.
The result suggested that Mr O'Brien gained support from at least five Coalition MPs as well as six crossbenchers and 64 Labor MPs.
Llew O'Brien is congratulated by Deputy Prime Minister Michael McCormack after being elected deputy speaker in the House of Representatives.Credit:Dominic Lorrimer
The ballot camehours after Mr O'Brien showed his unhappiness with Mr McCormack's victory by declaring he would not sit with the Nationals although he would continue to vote with the government.
The move foiled the government plan to elevate Mr Drum,the Nationals MP for the seat of Nicholls in Victoria and one of Mr McCormack's allies in last week's leadership spill.
In a separate ploy,Mr Joyce was preparing to nominate Mr O'Dowd to the Deputy Speaker position in a rebuff to Mr McCormack and Mr Morrison,but the plan was overtaken by Labor's nomination.
Mr Morrison greeted the vote by declaring it a victory for a government supporter.
Llew O'Brien was congratulated by Scott Morrison after the vote.Credit:Alex Ellinghausen
"There is no shortage of government members in this house to ensure that we continue to deliver on the promises we made to the Australian people,"the Prime Minister told the chamber.
But Opposition Leader Anthony Albanese said the outcome revealed the Coalition was in chaos.
"No amount of marketing or spin can hide the humiliation for the government from that ballot,"Mr Albanese said.
The Age andThe Herald revealed on Monday the Morrison government would take a new long-term emissions strategy to the UN Climate Change Summit in Glasgow in November,potentially joining about 80 nations to pledge net-zero carbon by 2050.
Energy and Emissions Reduction Minister Angus Taylor said the government expected to take a new strategy to the summit,which would be informed by its technology roadmap.
Liberal MP Trent Zimmerman endorsed a net-zero carbon target,in line with British Prime Minister Boris Johnson's plea to leading economies.
"We need to do the due diligence and we need to work out how we get there. I think it's very easy to say yes,"Mr Zimmerman said.
Loading
But Liberal senator Eric Abetz warned against a commitment to net-zero emissions by 2050,saying it was based on the"emotion and not about the substance of the issue".
Australian National University Emeritus Professor Will Steffen said whatever technology the new strategy deployed,the Morrison government must rule out all new fossil fuel development to meet the key goal of the Paris agreement and keep global warming to below two degrees.
"We can have no new fossil fuels,no extension of coal,no new gas… all must be banned if you are serious about Paris,"Professor Steffen said.
"Meeting 1.5 degrees (Celsius) is virtually impossible now,we've burnt too much carbon already. But what we can do is limit warming to around two degrees,"he said.
"To stay within two degrees we need to reach net zero emissions by 2040 - 2045 at the very latest - 2050 is too late,we've already put too much carbon into the atmosphere.
"We need to act as a global community and Australia,as the 16th biggest emitter must play its part,to reduce carbon emissions by 50 per cent by 2030 to stay within two degrees warming."