The Association of Management, Administrative and Professional Crown Employees of Ontario says its members voted 71 per cent in favour of the deal, which includes a two-year wage freeze.
The province says the agreement also calls for the restructuring of merit pay, short-term sickness benefits and time-off provisions.
It says the contract will bring savings of $55 million over two years.
The government had initially set a deadline of Sept. 9 for a new collective agreement with the union, after engaging in negotiations since early in the summer.
In August, the union had tabled an offer which included the wage freeze and other proposals to reduce the cost of administering the collective agreement but it was rejected by Queen's Park.
The workers had been without a contract since March 31.
For the past few months, the governing Liberals have been warning public sector unions of possible wage freezes as part of their efforts to eliminate the province's $14.4 billion deficit.