Whiteside, 33, appeared in 12 games with San Francisco this season, batting .091 (1-for-11).
Whiteside spent most of the year at Triple-A Fresno, batting .224 with one home run and 20 RBIs in 60 games, catching 36.2 percent (25 of 69) potential basestealers.
Originally selected by the Orioles in the sixth round of the 2001 First-Year Player Draft, Whiteside has appeared in 208 career Major League games with the Orioles ('05) and Giants ('09-12), batting .215 (105-for-489) with 21 doubles, 10 home runs and 43 RBIs.
Whiteside will join a group of Yankees catchers that currently includes Chris Stewart and Francisco Cervelli, who appeared at the Major League level in 2012, as well as prospect Austin Romine, who is playing in the Arizona Fall League after losing much of this past season to injury.
The Yankees have also expressed a level of interest in re-signing Russell Martin, who has served as New York's starting catcher for each of the last two seasons.