The agreement, reached on Tuesday morning, means the federal government's plans to wind back negative gearing and the capital gains tax discount will pass parliament by Thursday.
It allows the government to avoid a potentially lengthy delay when politicians leave Canberra for the five-week winter break.
In a last-minute concession to the Greens, Prime Minister Anthony Albanese agreed to stop people dodging the capital gains tax increase by buying property using money borrowed through a self-managed super fund.
The tweak would raise roughly $50 million extra for the government over the next four years, Treasurer Jim Chalmers said, but pushing back the NDIS overhaul would cost a few hundred million dollars.
The investment change was slammed by the head of the Self Managed Super Fund Association, who said any changes should have been grandfathered and needed additional consultation.
"Many investors and self-managed superannuation fund trustees have made legitimate financial commitments based on the existing rules," chief executive Peter Burgess said in a statement.
Greens leader Larissa Waters said the reforms were welcome progress but overall a missed opportunity to fix Australia's housing crisis.
"It could have been so much better, but it is a small step in the right direction," she told reporters in Canberra on Tuesday.
Liberal frontbencher Dan Tehan used question time to accuse the government of "taxmaxxing" with the Greens, while Opposition Leader Angus Taylor promised to repeal the changes if he were to become prime minister.
"Under this government... we see an assault on aspiration, a war on ambition," he told a parliament house press conference.
Super funds are protected from the tax changes, which will remove the 50 per cent discount on the capital gains tax for established properties and replace it with indexation of the cost base and a 30 per cent minimum tax.
SMSFs will be banned from using limited recourse borrowing arrangements, which allow trustees to borrow for a property while protecting the rest of the fund's investments from lenders if they default.
The Greens have argued closing the loophole prevents investors flocking to SMSFs to purchase tax-advantaged properties.
The changes will be extended to all assets, including businesses, although the government has announced a carve-out for innovative firms to placate the startup sector, which has complained it would be uniquely impacted by the new arrangements.
But those carve-outs will not be included in this week's tranche of legislation, but will instead be passed in a future bill before the changes take effect in 2027.
The bill also includes abolishing negative gearing for established properties, a $250 per year tax offset for workers and a standard $1000 deduction for work expenses.
As part of the Greens' deal, the treasurer will also have his powers to extend the 50 per cent discount to more assets reined in.
In exchange for the Greens' support of the tax changes, the government also agreed to extend an inquiry into controversial disability reforms.
The overhaul aims to rein in the spiralling $56 billion cost of the NDIS by kicking hundreds of thousands of people from the scheme.
A snap three-day probe inquiry's final report on changes to the scheme was due to be tabled on Tuesday after two extensions were granted.
However, an interim version is expected to be tabled instead, with the committee now set to deliver a final report by August 14.
Delaying the report would grant more time to build pressure on both Labor and the Liberals to withdraw support for the bill entirely, the Greens said.
The government has also agreed to amendments that will limit ministerial powers to cut recipients' budgets, ensure greater transparency on automated decision-making and prevent recipients from being forced to undergo restrictive practices to gain access to the NDIS.
