Minister of Higher Education Pierre Duchesne reinstated $26.5 million of that fund for one more year.
"We understand that it is a crucial question," he said.
Now, critics from opposing parties say the Parti Québécois is admitting it made a mistake by reimbursing the money.
The Liberal Party's interim leader Jean-Marc Fournier said the Marois government is improvising.
"They improvise because they have no vision on governing, they have no vision on economics. They don't think about the consequences," he said.
"They chose to cut, and after that they say 'Well, we're going to reimburse a third of it. Are you happy?' No. Why did you cut it in the first place?"
Quebec Premier Pauline Marois said the Liberals left behind an undisclosed budget shortfall of more than $1.5 billion.
The PQ said it was forced to slash the research fund as a result.
Coalition Avenir Québec leader François Legault said the funding should be fully reinstated on a permanent basis.
"Research is profitable for Quebec. It's profitable for our economy," he said.
After this year, universities, teaching hospitals and other think tanks will most likely have to turn elsewhere to replace the funding.
Nevertheless, researchers in medicine are welcoming the PQ's reversal.
"It's very good news for our patients and very good news for the population in general," said Dr. Serge Rivest, a health scientist at the Quebec University Hospital Centre.
The Quebec Health Research Fund lost $10 million under the PQ's initial cuts.
Researchers said laboratories could be forced to close and research projects could be put on hold indefinitely without the fund.