The Nationals received a jolt of validation today as Baseball America, known widely as a bible for prospects, named their farm system the best in all of baseball in its annual Prospect Handbook. The recognition came five years after the Nationals’ system ranked 30th — dead last.

“This is a huge day,” General Manager Mike Rizzo said. “We should make a big deal of this. It’s probably more important to me than a lot of other GMs.”

Rizzo, an executive who climbed the scouting ladder from the time his short-lived playing career ended, called the recognition “the epitome of a team award.” He credited every level of the operation, from ownership for the financial commitment to sign draft picks to minor league managers and coaches.

Rizzo gave special mention to the lowest-level scouts, in part because “I was that grunt area scout making $14,000 a year. They miss birthdays. They miss anniversaries. They’re on the road 150-200 days a year working for me. When the team is in Washington and you’re based in Southern California or Macon, Ga., this is something really great to read.”

Baseball America settled on its rankings, due to deadlines, before the Nationals traded four of their best prospects — pitchers A.J. Cole, Brad Peacock and Tom Milone and catcher Derek Norris — to the Oakland Athletics for left-hander Gio Gonzalez, but that does not diminish the accomplishment. As Rizzo has pointed out, the depth in the Nationals’ system allowed them to acquire a 26-year-old all-star whom they can place at the top of their rotation for at least the next five years.

Even after the deal, the Nationals have one of the strongest systems on baseball, topped with 2010 first overall pick Bryce Harper and stocked with several other players signed out of the draft using contracts well above the “slot” value recommended by Major League Baseball. Jim Callis, Baseball America’s prospect guru, said the Nationals will still likely be ranked between No. 5 and 10 when the magazine updates its rankings this spring despite losing four of their top 13 players.

“It’s nice tribute to the work they’ve done,” Callis said. “It’s no secret the draft is the most cost-effective way to build a team. It’s obvious the Nationals have been aggressive and taken advantage.”

The Nationals viewed the ranking as validation of the goals the Lerner family outlined upon taking over the team in 2006. While their payroll has remained below the league average and they took up residence at the bottom of the standings, the Nationals asked for patience and promised results. Under Rizzo, a former scout and scouting director, the Nationals committed to spending in the draft like few teams in baseball. They believe the strength of their farm system, now starting to pay dividends in the majors, is the result.

And so, Rizzo took a moment to celebrate. He sent an e-mail to his baseball operations staff, thanking and praising them.

“I want to congratulate each and every one of you because this honor belongs to you,” Rizzo wrote in the e-mail, a copy of which was forwarded to The Washington Post. “I am well aware that this achievement is the direct result of a Scouting & Player Development staff that is the best in baseball. I want to personally express my thanks for the grueling hours, endless miles, and huge workload you’ve taken on.”

The Nationals’ good fortune of drafting first in 2009 and 2010 helped build their system, but their philosophy and commitment to the draft, Callis said, played the largest role. The Nationals signed high-ceiling prospects such as Anthony Rendon, Alex Meyer, Brian Goodwin, Matt Purke and Sammy Solis with later picks using shrewd scouting and a willingness to break the bank on signing bonuses.

“It’s a credit to ownership, it’s a credit to the front office, it’s a credit to scouting,” Nationals Director of Player Development Doug Harris said. “We’ve got a really great group. [Rizzo] empowers his men and gives them autonomy to do the job. Our system isn’t just better at the top. It’s better throughout.”

The Nationals’ rise from last to first came despite no major trade acquisitions through trading veteran players for young talent, which Callis described as rare. (The Nationals acquired catcher Wilson Ramos by trading Matt Capps, but he no longer counts as a prospect.) He compared it to how the Brewers rebuilt their farm system through the draft last decade.

“It’s easier to rise up our rankings when you’re making trades,” Callis said. “They really haven’t done that. ... . . They were smart [in the draft]. They took full advantage of the rules in place.”

The full fruits of their effort will reveal itself on the field in seasons to come. But for now, the Nationals can take satisfaction in their rare recognition.