A person familiar with the negotiations told The Associated Press that the referees voted on the deal last week. The person spoke to the AP on the condition of anonymity because those details were confidential.
Owners ratified it at their meeting in Dallas on Thursday, and terms of the contract were not disclosed.
The agreement heads off the potential of two NBA lockouts. Players and owners still are working on a deal to replace the one that expired June 30.
"We did not get everything we wanted, but given the current economic climate and the continuing players' lockout, we are satisfied that this deal was in the best interests of our members," National Basketball Referees Association general counsel Lee Seham said in a statement.
The referees' contracts traditionally have been for five years, but they sought a two-year deal in 2009, hoping they could quickly renegotiate when the economy had improved.
Those negotiations went poorly, with the league locking out the referees on Sept. 18, a little more than two weeks after their contract had expired. Replacement referees were used during pre-season games, to the criticism of many coaches and players, before the sides agreed to a deal in time for the regular season.
These talks also had some rocky moments.
NBRA executive board member Thomas Washington called them a "long and arduous process." Seham said the referees' union intended to withdraw all pending contract grievances and charges before the National Labor Relations Board.