Jones had asked for a salary of $2.5 million.
Concurrently, the Pirates announced an agreement with Casey McGehee on a 2012 contract, settling both their own and MLB's last of 142 arbitration cases.
The decision in Jones' case fixed the final 2012 arbitration standings at 5-2, in clubs' favor.
Terms of McGehee's contract weren't immediately known. In figures filed in the event of a hearing, he had asked for $2.725 million, and the club had countered with an offer of $2.35 million.
The favorable decision in the Jones case snapped a long arbitration losing streak for the Pirates, who had lost the most recent hearings involving their players -- to infielder Jack Wilson in 2004 and to pitcher Ross Ohlendorf last February.
Jones and McGehee will begin competing for the Bucs' first-base job when the full squad reports to Pirate City on Feb. 24. Pitchers and catchers are reporting on Saturday, and will have their first workout on Sunday.