The club announced the agreement on Tuesday night.
Jones made $3.25 million last season, when he hit .280 and set career highs in games (151), doubles (26), homers (25) and RBIs (83). The 26-year-old also stole 12 bases and was voted Most Valuable Oriole by members of the media.
Jones was seeking $7.4 million and the Orioles were offering $5 million, but the sides managed to avoid an arbitration hearing scheduled for Friday.
Jones can earn performance bonuses of $25,000 each for 620 and 635 plate appearances. If he reaches both totals, he would get to the arbitration midpoint of $6.2 million.