All players implicated in December's Mitchell Report on performance-enhancing drugs were given amnesty as part of the agreement, the third major modification since the program was instituted in 2002 following accusations players were abusing steroids.
"It is time for the game to move forward," commissioner Bud Selig said. "There is little to be gained at this point in debating dated misconduct and enduring numerous disciplinary proceedings."
Thus, the deal eliminated 15-day suspensions assessed against Jose Guillen and Jay Gibbons.
Friday's agreement also ensures there will never be another Mitchell Report, as both sides agreed to keep players' names private until discipline is imposed in any future probe. The sides also agreed a player would be given any allegations and evidence against him before any investigatory interview.
Many players, including seven-time Cy Young Award winner Roger Clemens, complained Mitchell never disclosed the case against them until the report was released.
Talks to amend the drug agreement were prompted by the Mitchell Report's scandalous allegations, including those by Brian McNamee, the former personal trainer who testified under oath that he injected Clemens with steroids and human growth hormone.
Mitchell made many recommendations that Major League Baseball adopted unilaterally, and Friday's agreement covered the changes subject to collecting bargaining. In the deal, baseball will impose certification standards for strength and conditioning coaches starting next year.
Baseball, however, did not heed advice from the World Anti-Doping Agency to turn over testing to an outside agency.
Instead, the Independent Program Administrator, a position created in November 2005, will be given an initial three-year term and can be removed only if an arbitrator finds cause. Until now, he could be fired at any time by either side.
In addition, the decision over whether a player can be subjected to reasonable-cause testing will remain with management and the union, with any disagreement decided by the sport's regular arbitrator. Also, a joint management-union body called the Treatment Board will supervise the part of the program relating to drugs of abuse, such as cocaine.
Reps. Henry Waxman and Tom Davis, leaders of the House Committee on Oversight and Government Reform that has held hearings on drug use, said in a joint statement they were "pleased that MLB has taken steps to strengthen its drug-testing policy."
Yet the changes were not enough for Dr. Gary Wadler, chairman of the committee that determines WADA's banned-substances list.
"It's another incremental step. It's better than it was but not where it needs to be," said Wadler, who faulted baseball for not adding blood testing for human growth hormone and for not turning over testing to the U.S. Anti-Doping Agency.
"This still falls significantly short of the mark, no matter what internal bureaucracy they've patched together," Wadler said.
As part of the agreement, players will join MLB's efforts to educate youth about performance-enhancing drugs, and their union will contribute $200,000 to an anti-drug organization.
In exchange for those two provisions, Selig agreed not to discipline players implicated by Mitchell during the former Senate majority leader's 20-month investigation.
"We are gratified that commissioner Selig chose to accept Sen. Mitchell's recommendation that no further punishment of players is warranted," union leader Donald Fehr said. "In many instances the naming of players was punishment enough; in others it may have been unfair."
Guillen and Gibbons were suspended Dec. 6 following media reports linking them to performance-enhancing drugs. Those penalties, announced one week before Mitchell issued his report, were put on hold March 28 as negotiators neared an agreement.
"I'll put this behind me and move forward," Guillen said, still refusing to address the allegations. "I'm happy it's over with."
Players and owners reached their first joint drug agreement in August 2002, then under pressure amended it in January 2005 and instituted a 10-day penalty for first offenses. After Congress pushed for more changes, they amended it a second time in November 2005, increasing the first offense to a 50-game suspension, banning amphetamines and creating the IPA, who shared power with a management-union Health Policy Advisory Committee.