Finance Secretary John Swinney boosted funds by £10 million in the next financial year in a sector which was facing a £34.6 million cut.
The new total college fund of £522 million in 2013-14 will be matched in the following year, raising the level from an expected £471 million.
Mr Swinney announced the changes, which included more money for housing, during the passage of the Scottish Government's Budget Bill, which was agreed by 68 votes to 56.
Labour, Tory and Liberal Democrat MSPs all criticised the spending plan, while the National Union of Students (NUS) immediately branded the 2013-14 college cut, which amounts to £24.6 million, "damaging".
Following the vote, Mr Swinney said: "Within the constraints of devolution, our Budget prioritises construction, skills, employment and a green economic stimulus.
"We have taken steps to mitigate the damage being done by Westminster welfare reforms and to make sure our public services are fit for the future.
"Through immediate infrastructure investment we are providing a boost to Scotland's construction sector and wider economy and we are also maintaining the most supportive business environment in the UK.
"This is what we are able to do with the limited powers at our disposal. With the full fiscal and economic powers of independence, the Scottish Government could do even more to strengthen our economy and create jobs."
Mr Swinney pledged an extra £38 million for housing, saying the money will help provide new homes and improve existing stock.
The money will be split, with £10 million for "affordable" homes, £4 million to adapt and improve homes and £24 million for green energy schemes.
Other areas for investment include £10 million for trunk road maintenance and a plan to help town centre regeneration.
Housing providers will be able to access a £2 million fund to help test the development of affordable housing in vacant town centre properties.
Entrepreneurs could also benefit with an extra £1 million, doubling a fund to help businesses grow when they struggle to access finance.
But Robin Parker, president of NUS Scotland, said the college budget is disappointing.
"We fear that a cut of £24.6 million could see damage to students and to colleges, coming at the same time as colleges are merging and huge structural change," he said.
He noted the "positives" of fee-free tuition and the overall two-year increase, but added: "We need to ensure colleges can get through this year without damage to students and we fear cuts on this scale could have really negative consequences."
In contrast, John Henderson, chief executive of Colleges Scotland, said he "warmly welcomed" the additional £61 million over the two years.
"This additional funding will help to give colleges stability over the next two years while they work to successfully complete the reform process," he said.
"As the sector's representative, we have highlighted its economic importance to the Scottish Government and we are pleased that its value has been recognised by ministers."
Mr Swinney indicated last year where much of the available £28.4 billion Budget would be spent.
Billed as a Budget for growth, he announced money for a new energy skills academy and an employer recruitment scheme designed to help create up to 10,000 jobs for young people.
But Labour finance spokesman Ken Macintosh said it was difficult to find words to describe the Government's spending plans.
"It's difficult, except to use the word disappointing," he said. "Yes, there have been a few announcements this afternoon, but if John Swinney expects the country to be grateful for the fact he has not quite fully restored the cuts he made last year, then he has got another think coming."
Tory finance spokesman Gavin Brown MSP said the SNP had failed to genuinely prioritise the economy.
"All the detrimental decisions in this Budget are political ones by the SNP, merely designed to curry favour with the electorate rather than give a vital boost to the economy," he said.
"We asked for action in four key areas, and in all these areas the Scottish Government has come up short."
LibDem leader Willie Rennie said one of his ambitions was to restore the college fund.
"That's why I found it astonishing when there was celebration on the SNP benches when a cut of £25 million was announced. That's nothing to celebrate," he said.
Green co-convener Patrick Harvie criticised the "substantial" cut to colleges, and what he called a lack of environmental awareness in the transport budget.
"Just 3.6% of the transport budget will be on projects that reduce CO2 emissions," he said.
"Every single member in this Parliament has voted in favour of the climate change targets that we have set ourselves, and every single SNP member I've heard talks about them in crowing terms about global leadership."