"On the heels of one of the most competitive and exhilarating baseball games in our club's history, it is extremely unfortunate that the irresponsible actions of one individual would detract from the game on the field and tarnish an otherwise memorable night," the team said in a statement released Wednesday.
The team said it will "enact heightened security measures and alcohol policies that will ensure the fan experience and safety of everybody involved."
The man alleged to have thrown the can has come forward. The incident occurred in the seventh inning of the Blue Jays' 5-2 win.
Toronto police said they were investigating and on Wednesday evening released a photo of the man they alleged was responsible, urging him to turn himself in.
"I contacted Toronto police ... and identified myself as the person in the photo," Ken Pagan wrote in an email to The Canadian Press, adding he "cannot say much else."
The Toronto Sun says it has identified the man in the photo as Pagan,who says he is in the picture but did not throw the beer.
The Blue Jays said that the "individual responsible is not welcome back to the stadium." Team spokesman Erik Grosman said Tuesday that the fan was not ejected because he took off before police had a chance to nab him.
Major League Baseball has spoken with the Blue Jays about banning cans from the seats at Rogers Centre.
"We've also talked to the Blue Jays about the policies with respect to the serving of alcohol," MLB commissioner Rob Manfred said. "No cans, those sorts of things, to make sure that we have as positive an environment going forward as possible."
The Toronto Sun, which said Pagan was an employee of Postmedia and formerly of Sun Media, reported earlier Wednesday night it had contacted Pagan and that he suggested the police might not have it right, saying he was "drinking out of a cup."
The newspaper, owned by Postmedia, also reported that Pagan suggested that the pictures on Twitterindicate he had a cup in his hand after the can was tossed.
"I'd love to tell you what happened and my story ... but I can't say anything," Pagan said.
As Kim settled under a fly ball off the bat of Melvin Upton Jr., the can sailed past him and landed on the turf. Baltimore center fielder Adam Jones angrily pointed into the stands and yelled into the crowd.
Baltimore manager Buck Showalter emerged from the dugout and walked all the way to left field to register his displeasure with the umpiring crew before returning to the dugout.
"Someone threw a beer down at my player," Jones said. "That's about as pathetic as it gets between the lines. You don't do that. I don't care how passionate you think you are. Yell, cuss, scream, tell us we're horrible. We get that. We're the opposition. We completely understand that. To throw something at a player, that's as pathetic as it gets."
"Something like that should never happen. It's the first time for me and hopefully the last," Kim said through an interpreter.
In the confusion that followed, Jones said he and Kim were taunted with racial slurs.
"I've heard that so much while playing baseball, I don't even care," Jones said. "Call me what you want.
"We hear everything -- people cussing you and flipping you off. I get it. That's fine. We're here to play baseball, nothing more, nothing less. And to put us in harm's way just isn't part of the game. It's not part of any sport."
The Blue Jays said the safety of fans, staff, players and visiting teams was "paramount" and promised to bring in "heightened" security measures and alcohol rules for future games, though it did not provide details.
"We hope the focus will remain on the exciting play on the field, and that our fans will express their passionate support for the Blue Jays while demonstrating a level of respect and responsibility that has made Rogers Centre one of the best atmospheres for families and fans of baseball," it said.
A number of baseball fans took to Twitter to express their outrage, and distance themselves from what many called "inexcusable" behavior.
Toronto Mayor John Tory, speaking on CFRB radio, called the fan a "loon ball."
Though Manfred referred to it being a "rare ... event in one of our ballparks," this was the third such incident at Rogers Centre in the past three years.
Blue Jays fans tossed bottles and debris on the field during Game 5 of last season's AL Division Series against the Texas Rangers. The fans were upset by the call that let Rougned Odor score from third after catcher Russell Martin's throw back to the mound deflected off Shin-Soo Choo's bat.
In May 2013, a Blue Jays fan threw a drink at Orioles outfielder Nate McLouth during a game at Rogers Centre.
Information from ESPN's Jerry Crasnick, The Associated Press and The Canadian Press was used in this report.