Hernandez, 21, hit .249 with an OPS of .701 for Class A Bowling Green in the Midwest League this past season.
"Our scouts really liked him. The reports were good," D-backs senior vice president of baseball operations De Jon Watson said. "I think the catch-and-throw is Major League ready now, I think the bat is a little behind. So I think that's the one area we'll have to try and assess and evaluate during Spring Training, but we're excited about getting a young catcher that has tremendous upside and game-calling ability. We think he's got a chance to be somebody."
The D-backs had to pay $50,000 to select Hernandez, and he must be kept in the Major Leagues for the entire 2015 season or be offered back to the Rays for $25,000. It is also possible that the two teams could work out a trade, which would free the D-backs up to send him to the Minors if they choose.
It sounded like the Rays would ask for a good return if they were to make a deal.
"We had him projected in high [Class] A," Rays farm director Mitch Lukevics said of Hernandez staying in the big leagues all year. "So I would say that would be a reach on our evaluation. They have to stick. They have to make the 25-man Major League roster. And I hope we get him back."
As a 17-year-old, Hernandez had an epic Venezuelan Summer League season in 2011, hitting 21 home runs in 69 games.
"If that guy shows up in Spring Training, then look out," Watson said. "It will be fun to watch this young man come into camp and compete. This is his first opportunity to be in a big league setting where he's actually competing for a spot on the roster."
The D-backs selected right-hander Tim Crabbe from the Reds' organization in the Triple-A portion of the Draft.
"He's 90-94 [mph], spins a breaking ball, throws a changeup, has some upside," Watson said.
The 26-year-old had a 4.13 ERA in 30 games (12 starts) this past season for the Reds' Triple-A affiliate in Louisville.
Steve Gilbert is a reporter for MLB.com. Read his blog, Inside the D-backs, and follow him on Twitter @SteveGilbertMLB. This story was not subject to the approval of Major League Baseball or its clubs.