The deal was reached Friday night, hours after Estrada filed for arbitration, general manager Josh Byrnes said on Saturday.
Estrada, who made $460,000 last season, hit .261 with four home runs and 39 RBIs. In 2004, he made the NL All-Star team, batting .314 with nine homers and 76 RBIs.
Four other Arizona players filed for arbitration: second baseman Orlando Hudson, shortstop Alex Cintron and pitchers Brandon Lyon and Claudio Vargas. They will exchange proposed salaries with the Diamondbacks on Tuesday if they don't reach deals before then.