The association made the announcement in a release on Tuesday, saying that Weiner will continue to work on a daily basis, and "he looks forward to making a full recovery."
Weiner, 50, a longtime counsel for the MLBPA, was named executive director in December 2009 after Donald Fehr announced his retirement earlier that year.
Weiner was the lead negotiator when the Collective Bargaining Agreement was reached in 2006, and had a prominent role in the 2011 agreement as executive director.
"On behalf of Major League Baseball and the 30 Major League clubs, I send my best wishes to Michael Weiner and his family," Commissioner Bud Selig said. "I have great respect and admiration for Michael, with whom we have had a very constructive relationship both professionally and personally. This relationship has been a great benefit to baseball and has led to the tremendous success the game now enjoys. All of us look forward to Michael's full recovery and to his continued contributions to our game."
According to the Players Association website, more than 230 different players attended at least one bargaining session on the way to negotiating a deal that was highlighted by league realignment and postseason expansion, among other topics. That deal will ensure uninterrupted play through 2016.
Weiner graduated from Williams College in 1983 and Harvard Law School in 1986. He joined the Players Association in September 1988, and served as general counsel from 2004-09.