Partners HealthCare System has struck a new four-year contract with insurer Harvard Pilgrim Health Care that both sides said will help control Massachusetts health care costs by putting Partners’ large hospitals and doctors practices on budgets and limiting future reimbursement increases to between 2 and 3 percent annually, roughly the rate of inflation.

The contract is retroactive to Jan. 1 and will run through 2015. While the new “global payment” arrangement takes effect immediately, Partners doctors and hospitals this year will still receive payment increases allowed under the old contract — about 5 to 6 percent.