Charging motorists for using using roads may be considered to achieve ambitious car use cuts, while the rail line to Fraserburgh and Peterhead could be re-opened.
A leading transport academic described the plans as “genuinely radical”.
Campaigners Transform Scotland said the move away from road building “demonstrably represents the end” of dualling the A96 in full.
The two parties said they would maintain “distinct positions” on fully dualling the A96, which the Greens oppose and which is due to be completed by 2030 at an estimated cost of £3 billion.
However, they have agreed on subject it to a "transparent, evidence-based review to include a climate compatibility assessment to assess direct and indirect impacts on the climate and the environment” to be completed by the end of 2022.
Parts of the scheme will go ahead, including the Inverness-Nairn section and bypasses of Nairn, Elgin, Keith and Inverurie.
Alongside those there will be additional public transport upgrades along the route, including further improvements to the Inverness-Aberdeen rail line “to make it more competitive to road” and bus priority measures on the A96.
Feasibility work will examine the re-opening of a rail line between Dyce and Ellon, Peterhead and Fraserburgh, and a possible “mass rapid transport system” for the region.
However, the deal said work on trunk road projects already under construction would continue, suggesting the £3bn A9 dualling between Inverness and Perth, which the Greens also oppose, has escaped the axe.
But the agreement also stated: “We agree that in the face of the climate emergency we need to shift away from spending money on new road projects that encourage more people to drive, and instead focus our money and effort on maintaining roads, improving safety and providing a realistic and affordable alternative through investing in public transport and active travel.
"New roads projects will normally only be taken forward where they reduce the maintenance backlog, address road safety concerns, or adapt the network to deal with the impacts of climate change or benefit communities such as bypassing settlements.”
The deal confirms the SNP’s target of cutting car use by 20 per cent by 2030, but “demand management options” will now be considered to help achieve it.
That suggests some form of what was previously termed road tolls or congestion charging might be looked at “to encourage the use of active travel and public transport as an alternative to cars”.
20mph speed limits will be introduced on “all appropriate roads in built-up areas” within four years, with a task group set up to plan “the most effective route to implementation”.
The pledge follows the defeat of a Greens’ bill in 2019 to make 20mph the default limit in urban areas across Scotland.
The agreement puts a date on the SNP’s pledge to increase spending on active travel – walking, cycling and wheeling - from 3 to 10 per cent of the transport budget.
It will rise form £115m a year to at least £320m by 2024-25.
Other agreed measures include:
- A “fair fares review” to “ensure a sustainable and integrated approach to public transport fares” because they are rising while the cost of car travel is falling.
- A pilot project enabling people to upload footage of dangerous driving to Police Scotland, which has been urged by campaigners Cycling UK and whose success elsewhere in the UK was referred to in the Scottish Government’s latest road safety strategy.
- Funding support for new buses may require them to have spaces for bikes as well as wheelchairs and pushchairs.
- A new community bus fund to improve local transport.
- The way Scotland’s ferries are run will be assessed to ensure “good outcomes for communities, value for money, accountability and transparency”.
- Renewed moves to devolve more powers over the railways to Scotland, which could clash with the UK Government’s plans to establish a single “Great British Railways” system.
Sustainable transport campaigners Transform Scotland said the “modest scaling back” of road building was long overdue.
Director Colin Howden said: “We’re pleased the current set of Scottish ministers are beginning to see the errors of some of the dinosaurs that preceded them.
"There’s certainly no case on climate change grounds for dualling the whole of the A96, so this demonstrably represents the end of that project.
"Even with a reduced spend on the A96, the Government’s transport capital investment plans still remain heavily skewed towards high-carbon infrastructure."
Scotland’s leading transport academic, Professor Iain Docherty of Stirling University, said: “Transport policy in Scotland has been moving away from accommodating the car and towards promoting public transport and active travel for some time.
"This agreement accelerates the shift.
"Planning deliberately for a future in which there is less rather than more car travel is genuinely radical and very different from recent statements by the UK Government.”