Toronto selected the pitcher with the 21st overall selection in the 2011 First-Year Player Draft. The native of Massachusetts will instead attend Vanderbilt University in the fall and is not eligible to re-enter the Draft until 2014.
The Blue Jays did sign right-hander Kevin Comer (No. 57 overall) and highly touted left-hander Daniel Norris (74) late Monday night.
"Obviously, you go into these things hoping to sign the players, but at the same time, you understand that there's no guarantees," Blue Jays general manager Alex Anthopoulos said on a conference call after the deadline passed.
"I think generally speaking, we're very pleased with the result. We had a lot of picks, we took a lot of [what] Draft experts deemed tough signs, and we were able to come to terms with pretty much all of them."
Toronto had a total of seven selections in the first 78 picks of the Draft, second in the Majors to Tampa Bay. Beede was the only one of the seven not to sign, and the Blue Jays will now receive the 22nd pick -- technically 21A -- in next year's Draft as compensation.
Beede also becomes the only player taken in the first round of the 2011 First-Year Player Draft that did not finalize a contract.
There appeared to be a large gap between the two sides during the final week of negotiations, and they never got close to getting something done. Beede was reportedly looking for $3.5 million, while the Blue Jays were willing to offer one million short of that.
"They were still far off," Beede told the Worcester (Mass.) Telegram and Gazette. "They ended up getting to $2.5 million, but that still wasn't what we valued the Vanderbilt education at. It was obviously the hardest decision I've ever had to make, but I'm tremendously excited."
The 18-year-old Beede is a 6-foot-4, 200-pounder from Auburn. His fastball ranges from 86-93 mph and he possesses an above-average curveball and changeup.
Beede is the son of former professional baseball player Walter Beede, who was selected in the 13th round of the 1981 Draft. Walter reportedly provided his son with the type of elite coaching that taught him how to throw a curveball by the time he was 13.
The big right-hander led his high school team in Auburn, Mass., to a state championship in 2009. He then transferred to the more competitive Lawrence Academy, where he went 14-1 with a 0.80 ERA while striking out 189 in 96 1/3 innings over two seasons.
Anthopoulos declined to get into specifics regarding the Beede negotiations. Instead, he spoke about the club's general philosophy regarding negotiations with Draft picks.
The Blue Jays put a set value on players, and if the two sides can come to terms, all the better for the organization. If not, the club is prepared to walk away and accept a pick in the following year's Draft as compensation.
"I've always felt when it comes to the draft, I don't know that there's a whole lot to negotiate," Anthopoulos said. "I will never tell someone that they're wrong about what they're going to be.
"If somebody wants to tell me they're going to be an MVP candidate, I tell them you very well may be right, we'll find out in five years."
Toronto signed 35 of the 55 players it took in the Draft. Norris and Comer were joined by infielder Christian Lopes and third baseman Matt Dean as signees on the final day.
Norris was considered a tough sign because of his commitment to Clemson University, but he ended up inking a deal for $2 million.
The 6-foot-2, 170-pounder was seen as one of the top left-handed high-school pitchers in the Draft, but he fell to the second round because of his stance on attending school.
Norris has a plus fastball, which averages around 92 mph, that he uses to set up his hard curveball and changeup. Scouts have been impressed with his mound presence and project Norris as a No. 3 starter in the Major Leagues.
"I think with what we paid Daniel Norris, I think it's definitely reflected in his bonus, but that's as far as we were going to take it," Anthopoulos said. "There's no question Daniel Norris should not have been a second-round pick.
"He was absolutely a first-round talent, but he slid because of some signability concerns, and that was an opportunity for us."
Comer appeared set to join Beede at Vanderbilt until he signed with Toronto for $1.65 million. The native of New Jersey is a 6-foot-3, 205-pound starting pitcher from Seneca High School. He reportedly throws 90-94 mph with an upper-70s offspeed pitch that is a combination of a curveball and slider.
Anthopoulos would have preferred to sign all of his top picks, but said his club's inability to do so won't impact future Drafts.
"I think the model that we use going forward is what we've done here, and we're going to continue to do that," Anthopoulos said. "When you're going to be aggressive like this, I expect each year to have several players unsigned. But on the whole, I think we're going to come out ahead."