The Jays Care Foundation, the team's official charity, will receive a $10,000 grant from Major League Baseball as part of the recognition.
"The Toronto Blue Jays Baseball Academy program embodies the franchise's significant investment in the young people of Canada," said Commissioner Bud Selig. "The determination of the Blue Jays to provide thousands of children with the tools to succeed in baseball and in life has made a remarkable difference in not just Toronto but in many other communities as well, and Canadians should take great pride in their country's Major League Baseball team.
"I commend the Blue Jays and all of our clubs for embracing the game's essential social responsibilities and making a positive impact in their respective communities year after year."
The Toronto Blue Jays Baseball Academy concentrates on physical activity through baseball, as well as programs that provide resources and help develop life skills for youths. These programs are conducted through programs such as Rookie League, Field of Dreams projects, and Super Camps and Instructional Clinics. The award is for the team's multifaceted efforts in 2012.
"We are honored to receive the Commissioner's Award for Philanthropic Excellence," said Blue Jays president and CEO Paul Beeston. "We made an organizational decision several years ago to reach out to communities not just in Toronto but all across the country, as we recognized our responsibilities as Canada's only Major League team. The support we have received from all provinces has been overwhelming and it was imperative that our programs reflected that passion.
"The creation of the Toronto Blue Jays Baseball Academy, combined with the tremendous efforts of the Jays Care Foundation, has had a significant impact on the youth of the nation. We are very proud of this recognition and it speaks volumes to the efforts of many in our organization and our key partners, including Boys & Girls Clubs of Canada, Baseball Canada and Little League Canada. Together we have truly made a positive impact in our communities across Canada."
The Boston Red Sox received the Commissioner's Award for Philanthropic Excellence in 2010, and the Chicago White Sox won the award in 2011.
Thomas Harding is a reporter for MLB.com. Read his blog, Hardball in the Rockies, and follow him on Twitter @harding_at_mlb. This story was not subject to the approval of Major League Baseball or its clubs.