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.

If necessary, Partners will refund to Harvard Pilgrim any fee-for-service payments it received that result in total reimbursements for 2012 exceeding the budget established under the global payment set-up. That system -- which applies to the 60 percent of Harvard Pilgrim Massachusetts members who are in its health maintenance organization --gives medical care providers a set amount of money to cover all of a patient’s care annually, rather than reimbursing them for every visit, test, and procedure.

Responding to pressure to rein in rising medical prices, Boston-based Partners -- the state’s largest hospital and physicians organization -- has also torn up the last years of its previous contracts with two other large commercial health insurers: Blue Cross Blue Shield of Massachusetts and Tufts Health Plan. The renegotiated deals with Tufts and Blue Cross similarly called for annual payment increases of about 2 to 3 percent -- and shifted Partners hospitals into alternative payment models for some insurer’s members.

Contract negotiations between Partners and Harvard Pilgrim, based in Wellesley, took about nine months, according to Partners spokesman Rich Coppcq.