The Blue Jays gave up shortstop Yunel Escobar, catcher Jeff Mathis, infielder Adeiny Hechavarria, pitcher Henderson Alvarez, minor league pitcher Anthony DeSclafini and two top prospects -- outfielder Jake Marisnick and pitcher Justin Nicolino -- in return.
The deal was viewed in some quarters as a way for the Marlins, who finished last in the National League East the past two seasons, to lower their player payroll.
Selig said he came to his decision after consulting with others at MLB headquarters and elsewhere in baseball.
"After a thorough examination of this information, it is my conclusion that this transaction, involving established major leaguers and highly regarded young players and prospects, represents the exercise of plausible baseball judgment on the part of both clubs, does not violate any express rule of Major League Baseball and does not otherwise warrant the exercise of any of my powers to prevent its completion," Selig said in a statement. "It is, of course, up to the clubs involved to make the case to their respective fans that this transaction makes sense and enhances the competitive position of each, now or in the future."
He said he would keep an eye on the situation going forward.
Marlins owner Jeffrey Loria in a statement Monday the club is committed to "get back to our winning ways."
"It may not happen overnight, but with the players we acquired in the second half of last season, coupled with the infusion of players we are acquiring now, we will be returning to Marlins baseball: high energy and hungry," he said.
The Marlins won the World Series in 1997 and 2003.
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