Holder's bonus with the Yankees is reported to be $1.8 million, slightly below the pick valuation of $1.914 million. The 21-year-old was selected from the University of San Diego and has been rated as the best defensive shortstop in this year's Draft class.
• Yankees' Draft picks
"There's not a lot of guys that you say, 'I want to get there early to watch this guy take ground balls,'" said Damon Oppenheimer, the Yankees' director of amateur scouting. "That was what was special about him. His hands, the way he gets rid of the ball, multiple angles to throw, the carry on his throws.
• Draft Central
"I made sure I got there early in Cleveland to watch Omar Vizquel take ground balls, and this guy can do some of those things that Omar did between his legs and things."
As a junior in 2015, Holder was named the West Coast Conference Player of the Year after batting .348 (78-for-224) with 45 runs scored, 14 doubles, four home runs and 31 RBIs in 55 games for the Toreros.
Holder was taken with a compensation round pick obtained after right-hander David Robertson signed with the White Sox in December. Oppenheimer said that the organization believes that Holder will succeed offensively as a professional.
"He hit .348 in a really good conference out there; he had as many walks as strikeouts, which is important to us," Oppenheimer said. "The guy does not strike out, he had almost a 12-at-bat-per-strikeout rate, a .418 on-base percentage and a .900 OPS. Those aren't numbers to scoff at. From the left side, to go along with what he does defensively, he's going to be a fine offensive player to go along with some stellar defense at shortstop."
The Yankees' first selection was right-hander James Kaprielian from UCLA, who was No. 16 overall; the Yanks' highest selection in 22 years. Oppenheimer has said that the Yankees expect to reach an agreement with the 21-year-old starter, who is being represented by Scott Boras.
Bryan Hoch is a reporter for MLB.com. Follow him on Twitter @bryanhoch, on Facebook and read his MLBlog, Bombers Beat. This story was not subject to the approval of Major League Baseball or its clubs.