Mr Joyce backed a motion to strip net-zero emissions by 2050 from the party platform at its national conference in Canberra on Saturday.
The former party leader had previously brokered a deal to support it when in government with then-prime minister Scott Morrison.
Mr Joyce slammed the target but his bid to have the party abandon it ultimately failed when the motion was amended to remove reference to the policy.
It now calls upon the parliamentary team to "take a practical approach to lowering carbon emissions as a substantive move to nuclear power is made".
A vote for the amended motion will take place on Sunday.
Mr Joyce argued against stripping reference to net-zero, saying you couldn't oppose the methods required to get there - such as transmission lines and methane emission reductions - and support the target.
"It's just counterintuitive and counterfactual to what you have to do," he told the conference on Saturday.
"This is an issue that is moving politics ... because we can't wait.
"It's happening to us on the land right now and the crowds are growing and the anger is furious."
It was almost a direct rebuke to Nationals leader David Littleproud's opening remarks to the conference, which called for nuclear energy to reach the emissions target rather than scrapping it altogether.
"There is a pathway under a Dutton-Littleproud coalition-led government," he said.
"We're going to continue the pathway of accelerating the conversation around nuclear energy, the nuclear technology - that's zero emissions."
There were concerns dumping the target could undercut the Nationals' argument about using nuclear power as an alternative clean energy source.
One delegate told the conference getting rid of net-zero would hand Labor victory for the next decade as voters would not understand the nuances of moving to nuclear energy instead of meeting current renewable energy targets.
"They see us as (the) National Party just going in and wrecking the environment," the delegate said.
Another questioned why the party would give oxygen to the net-zero debate instead of pouring energy into opposing the voice referendum and putting Labor's feet to the fire over cost of living pressures.
Nationals Darren Chester, Susan McDonald, Anne Webster and Andrew Willcox voted to amend the motion to strip reference to abolishing the policy.
Mr Joyce, Matt Canavan, Colin Boyce and Keith Pitt voted to keep the focus on abolishing net-zero.
The leadership team of Mr Littleproud, Perin Davey and Bridget McKenzie abstained from voting.
Some rank-and-file members were furious at the decision to amend the motion and take out the push to abolish the policy.
"We're meant to be a membership-based party and they're not even letting the members have a debate," one party member told AAP on the condition of anonymity.
The debate has been enough for Mr Joyce to come under fire from his own party.
Questions have been raised by both Liberal and Nationals sources, speaking on the condition of anonymity, about the feasibility of Mr Joyce's shadow cabinet spot if he does not toe the line on net-zero.
Liberal MP Julian Leeser bowed out of shadow cabinet to campaign for the Indigenous voice against official policy.
Nationals deputy leader Ms Davey said she remained committed to what the party room decided with regards to net-zero in that the pathway would be "technology not taxes".
Mr Joyce again ruled out ambitions to return to the leadership for the third time amid speculation he is using the argument to undermine Mr Littleproud's position.
Asked about a potential threat to his leadership if the issue flared up, Mr Littleproud told reporters "you've probably got too much time on your hands".
Any motion passed at the party's annual conference is not binding on the parliamentary caucus.
Opposition Leader Peter Dutton said he remained committed to net-zero and maintained there was strong support for the policy.
