Professor Bryan MacGregor from Aberdeen University and Professor Murray Pittock of Glasgow University were speaking as a new campaign group, Academics for Yes, was launched ahead of the independence referendum in September.
The group - which is a rival to the pro-UK Academics Together - already claims to have some 60 members.
Speaking at its launch, Prof MacGregor told how the “negativity of the No campaign” had compelled him to make a public stand.
Academics Together, an off-shoot of the Better Together campaign, claimed last month that plans to continue to impose tuition fees on students from England, Wales and Northern Ireland after independence ‘would run into significant problems with European law’.
At the time, Professor Susan Shaw, former vice principal of Strathclyde University, said that meant the Scottish Government could only guarantee its policy on university tuition fees if the country stays in the UK.
Today, Prof MacGregor said: “I am not a politician. I am not even a political activist. I am an academic and I am a citizen. I had no intention of taking an active role and certainly not a public role in the referendum campaign.
“But the negativity of the No campaign has compelled me to make a public stand.”
Profs MacGregor and Pittock argued that a Yes vote in the referendum would “create improved and more secure funding” for universities.
They added: “Higher education is one of Scotland’s many success stories: our research is among the most highly cited in the world, and our Government ceaselessly promotes it.”
But they warned a vote to stay in the UK could result in funding cuts, adding that UK Independence Party (UKIP) success in this year’s European Parliament elections could lead to a loss of European funding for research.
The professors claimed: “The main threats from No are cuts in the Scottish block grant, loss of access to EU funding and overseas goodwill.”
They said the “relentless reduction in public spending” at Westminster would see a reduction in funding for universities south of the border - with a subsequent reduction for Scotland.
Meanwhile, any future change in the formula for allocating cash between the different parts of the UK “would have catastrophic effects on higher and further education expenditure in Scotland, putting pressure on any Scottish Government to re-introduce fees in Scotland”.
Prof MacGregor and Pittock said: “These outcomes would be disastrous.”
Orkney-based Donna Heddle, a professor at the University of the Highlands and Islands, added: ‘I’m backing this campaign because it’s the right thing to do. Independence is the only way that academia and research will flourish in Scotland.”
Yes Scotland chief executive Blair Jenkins hailed the members of Academics for Yes as being “an A-team from the various fields of learning”.
Mr Jenkins said: “Those involved have a wealth of knowledge and experience to bring to our ever-growing movement.
“Their views and advice form opinions that have serious relevance to a future Scotland - an independent nation - and their fears, worries and warnings must be heeded.”
A spokesman for Better Together said: “We can all look forward to some interesting debates taking place over the coming months between this new group and our well established Academics Together group.”