Federal Employment Minister Jason Kenney and Quebec Labour Minister Agnes Maltais made the announcement at separate news conferences Tuesday afternoon.
Ottawa and Quebec reworked a current labour market deal that will be valid for six more years.
It will have the same funding but be subject to more conditions.
"This includes all the advice we received from employers and unions in Quebec and it reflects the specificities of the Quebec model," Kenney told a news conference in Ottawa.
"It is proof of how open federalism can work, with the flexibility we have demonstrated."
Maltais said she was pleased to have received special status for Quebec.
"It respects the jurisdiction and the know-how of Quebec," she said in Quebec City.
Several observers had contended the lack of an agreement would help the sovereigntist Parti Quebecois government win a majority in a provincial election that is expected to be called Wednesday.
Federal NDP Leader Tom Mulcair said last Friday the conclusion of an agreement in principle on the Canadian Job Grant program with all the provinces and territories except Quebec would emerge as an election issue in the province.
Kenney said the announcement falling on the eve of a likely provincial election call is "pure coincidence."
He pointed out the federal government has no influence on provincial election dates and said a deal with other provinces was announced on Friday with no electoral pressure.
The Harper government has insisted that Quebec will have to be more accountable for the $116 million it will be getting.
The province will have to present data on employment outcomes more often and more financial data.
Ottawa wants to ensure that the funds go toward training and not more bureaucracy.
Quebec will also continue to involve employers closely in the training system.
Maltais' office said the conditions have not changed from the previous agreement.
Quebec had argued that Ottawa was interfering in provincial jurisdiction. It had wanted to be able to opt out of the job-training program with financial compensation.
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