The Newton Bar roundabout to the north of the city centre will be revamped with new pedestrian crossings, traffic lights, cycling lanes and carriageways for drivers.
The £9.5m scheme, most of which will be funded by West Yorkshire Combined Authority (WYCA), was bitterly opposed by campaign groups Just Transition Wakefield and Friends of the Earth, mainly because of the axing of trees on the roundabout and the pollution caused by more car journeys.
The latter even accused councillors of "greenwashing", as they slammed the new proposals to rewild a nearby plot of land as "tinkering around the edges".
But Wakefield Council insisted a "majority" is in favour of the plans and that abandoning them would force them to return money to WYCA, plus pay out up to £2m in compensation to contractors.
They also say the scheme will improve air quality overall and make life safer for everyone who uses the junction.
Councillor Michael Graham said he "sympathised" with the objectors, but that he disagreed with them.
Speaking at a Cabinet meeting on Tuesday, he said: "Everyone who's used it will know it's a nightmare roundabout to be on, especially at peak times.
"The traffic backs up for miles. It's one of the main ways into Wakefield and out of Wakefield.
"I think this will improve the air quality, but for me it's about safety as well."
On the prospect of having to give money back to WYCA if the scheme did not go ahead, Coun Graham said he'd "never be able to vote for giving £8.3m back to anyone".
He added: "Having to give up to £2m worth of compensation to developers as well, it's just not going to happen, I'm sorry.
"The vast majority of local residents want this to go ahead. They don't want us to be giving compensation to anyone.
"It's their money - taxpayers' money - and we need to be protecting it."
Linking Outwood, the A650 and Bar Lane, the junction is heavily used by motorists driving to and from Leeds, to Pinderfields Hospital and into the centre of Wakefield.
The revamp plans also include a memorial to the five police officers who died in a tragic bus crash at the junction in 1978 and a pit wheel, in a nod to the area's mining heritage.
The scheme had been due to start before Christmas but was delayed after protests from the green groups.
Deputy leader Councillor Jack Hemingway said the pause had been justified as the original scheme had been approved before the council declared a climate emergency in 2019 and a biodiversity emergency in 2021.
But he said the amended plans represented a "pragmatic way forward."
Councillors approved the new scheme unanimously, but agreed to explore the idea of transplanting mature trees onto the rewilding site, which will also feature a footpath for walkers.
That's because the 300 trees and 200 shrubs set to be planted there will be unlikely to grow to full length for many years.
Responding to the decision, Stuart Boothman from Just Transition Wakefield said: "We are deeply disappointed by the decision and fear the resulting
"We are not convinced by the predictions that congestion will be
"This is partly because of the multiple sets of traffic lights planned for the new junction, but mainly because much of the queuing is caused by congestion on Leeds Road and Wentworth Street as traffic queues into the city.
"There are other, more cost-effective ways to reduce traffic congestion.
"Further, if traffic flow does improve, road capacity and vehicle speeds will increase, increasing carbon emissions."
Local Democracy Reporting Service