Emaus became eligible for the Rule 5 Draft when he was left off the 40-man roster last month. The 24-year-old hit .290 with 15 home runs and 75 RBIs last season with Double-A New Hampshire and Triple-A Las Vegas.
"We knew that there was a high probability that we would lose him," Blue Jays general manager Alex Anthopoulos said. "At the same time, you have to go with your scouts and your player development staff. I know it's a compliment to the organization when you start running out of 40-man spots."
Emaus was originally drafted in the 11th round of the 2007 First-Year Player Draft by former GM J.P. Ricciardi, who is now an assistant GM with the Mets.
Emaus has shown the ability to hit for power at the Minor League level, but there are questions about whether that would translate well to the big leagues. He appears more likely to make the Majors as a utility player.
Toronto receives $50,000 from New York in exchange for Emaus. The Mets must keep him on their 25-man roster all season or offer him back the Blue Jays for $25,000.
Anthopoulos said the main reason his club did not make a selection in the Major League category was because it wants to hang onto the three open spots that are available on the 40-man roster. With the likelihood of adding free agents in the coming weeks, the three open spots became a premium.
"The guy we wanted got taken," Anthopoulos said while not naming anyone specific. "Then we didn't see anybody else ... that we felt was worth it, considering the fact that we feel like we're already going to have to start taking guys off the [40-man roster]."
Anthopoulos did opt to make a couple of selections during the Minor League portion of the Rule 5 Draft. He selected middle infielders Ivan Contreras (Triple-A Arkansas) and Roan Salas (Venezuela Summer League) for a cost of $12,000 each.
The 23-year-old Contreras, who was taken in the Triple-A phase, hit .257 with nine RBIs in 167 at-bats at three different Minor League levels last season in the Angels' organization. The Dominican Republic native was originally signed as a free agent in 2005.
Salas hit .345 with five home runs, 42 RBIs and 16 doubles in 60 games at Venezuela. He was the property of Tampa Bay.
"That's strictly based off our scouts," Anthopoulos said of the selections. "If we have a scout that believes strongly in someone, we don't have anything to lose. I'm a big believer that if you have a scout pounding the table for someone that's a Rule 5 Draft -- or a waiver claim or something like that -- you just got to go ahead and do it. ... If you can't do that for your scout, there's something wrong."