Napoli, 32, signed a one-year, $5 million contract before the season after a three-year, $39 million deal fell through over concerns the team had about his injured hips. With incentives, he ended up making $13 million.
Because of his degenerative hip condition, he converted from catching to playing first base.
Napoli had a batting line of .259/.360/.482 with 23 home runs and career-highs in doubles (38), RBIs (92) and plate appearances (578) over 139 games.
Before reportedly making the multiyear contract overture, the team made Napoli a $14.1 million qualifying offer, which he is expected to formally decline by Monday's 5 p.m. ET deadline.
Rodriguez's appeal hearing resumes Nov. 18 and could last at least five days. Assuming it ends at that point, arbitrator Fredric Horowitz is expected to take another 25 days to make a decision.
Yankees manager Joe Girardi said the drawn-out process complicates matters for the team as it looks to rebound from an injury-plagued season that resulted in 85 wins.
The Yankees reported that hitting coach Kevin Long and the rest of the team's coaching staff will return for the 2014 season.
Financial details of the agreement are not yet available, and Pena must still pass a physical, which will be performed on Tuesday.
Pena hit .297 with four homers in 71 games as the Detroit Tigers' backup catcher this past season. (Editing by Frank Pingue)
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