Dellin Betances and Ryan Pope, both right-handed pitchers, and infielder Brandon Laird are no longer available to be selected. New York's 40-man roster currently stands at 33 players.
Betances, 19, is widely regarded as one of the Yankees' elite pitching prospects. The Brooklyn-born hurler was 8-1 with a 1.77 ERA in 14 starts for Class-A Tampa this year, striking out 88 and walking 19 in 71 innings while allowing 43 hits.
An eighth-round Draft selection of the Yankees in 2006, Betances also made three starts at Double-A Trenton, pitching to a 3.77 ERA.
Pope, 24, pitched all of this season at Double-A, going 4-6 with a 4.20 ERA in 46 games (seven starts), finishing 27 games. In 94 1/3 innings, Pope -- a third-round selection by New York in 2007 -- allowed 88 hits while walking 31 and striking out 85.
Laird, 23, spent most of this year at Double-A, where he batted .291 with 23 home runs and 90 RBIs in 107 games. He also played 31 games at Triple-A Scranton/Wilkes-Barre, batting .246 with two homers and 12 RBIs.
A 27th-round pick by the Yankees in 2007, Laird played almost all of his games at third base. He was mentioned this week by general manager Brian Cashman among possible candidates to compete for a bench job during Spring Training.
Laird and Pope both represented the Yankees in the Arizona Fall League for Don Mattingly's Phoenix Desert Dogs.
The 40-man roster moves were necessary to protect the three players from the Rule 5 Draft, which will be held at the conclusion of baseball's Winter Meetings in Lake Buena Vista, Fla., on Dec. 9.
Any player who signed before the age of 19 and has played five professional seasons, or who signed after his 19th birthday with four professional seasons, is eligible to be selected in next month's Draft if not on the big league 40-man roster. The selecting team must pay a $50,000 fee and keep the draftee on its active roster for the entire season, with few exceptions.
The Yankees also announced Friday that they acquired Minor League outfielder Cody Johnson from the Braves in exchange for cash considerations and assigned him to the Triple-A Scranton/Wilkes-Barre roster.
Johnson, 22, batted .212 this season with 18 home runs and 60 RBIs in 106 combined games for the Gulf Coast League Braves, Class A Myrtle Beach and Double-A Mississippi.
Originally selected by Atlanta in the first round of the 2006 Draft, Johnson has a .243 (392-for-1,613) batting average in 456 career Minor League games with 94 home runs and 309 RBIs.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.