The changes will see fees for degrees the government believes will have more job opportunities drop, while other degrees like humanities and law will become more expensive.
Agriculture students are one of the biggest winners under the change, with the average cost of a three-year degree expected to fall from nearly $28 600 to $11 110.
The Federal Government will also allocate $400 million for new programs to help students from rural and remote areas and a $900 million fund for universities to improve ties with industry.
Universities are anticipating record numbers of applications for study in 2021 as the reality of the coronavirus-driven recession bites young people worst of all.
Youth unemployment has soared to 16.1 per cent, with young people's jobs making up 45 per cent of those lost in May.
Federal Education Minister Dan Tehan is offering to increase the number of university places by 39 000 over the next three years, rising to 100 000 more by 2030.
The Coalition had effectively capped places over the past couple of years by freezing its funding at 2018 levels.
The trade-off in the new deal is changing what students and taxpayers pay.
Fees would also be cut for teaching, nursing, clinical psychology, science, health, architecture, IT, engineering and English courses.
Those doing the more expensive degrees will be able to cut their costs by taking up courses in the cheaper, more "useful" areas.
No existing student will pay more.
The minister is putting pressure on universities to back the plan, which he says was designed in consultation with leaders from the sector.
The National Union of Students condemned the government's proposals, saying universities were not "job factories".
“While the lowering of fees in specific degrees is a positive opportunity for some students, this move is at the expense of hundreds of thousands of young people who have chosen to study a degree that the government doesn't deem worthy enough,” the union said.
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