All players implicated in December's Mitchell Report on performance-enhancing drugs were given amnesty as part of the agreement, which toughens baseball's drug rules for the third time since the program began in 2002.
"We are gratified that Commissioner Selig chose to accept Sen. Mitchell's recommendation that no further punishment of players is warranted," union head Donald Fehr said.
The independent 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.
But baseball did not heed advice from the World Anti-Doping Agency and turn drug testing over to an outside agency.
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 Major League Baseball has taken steps to strengthen its drug-testing policy."
Guillen and Gibbons were suspended in December after media reports linked them to performance-enhancing drugs. Those penalties were put on hold just before the season began as negotiators neared an agreement.
"It is time for the game to move forward," Selig said. "There is little to be gained at this point in debating dated misconduct and enduring numerous disciplinary proceedings."
The sides agreed that in future investigations, allegations against players won't be made public unless discipline is imposed, and that a player will be given the allegations and evidence against him before any investigative interview.
In the deal, the sides agreed:
• Annual tests will rise by 600 to 3,600, an average of three per player.
• As many as 375 offseason tests can be conducted over the next three years, up from the current limit of 60 per offseason.
• Testing will include the top 200 prospects for each year's annual draft.
• The independent administrator will issue an annual report detailing what substances resulted in positive tests, the number of tests given and therapeutic use exemptions by category of ailment.
• Additional substances were added to the banned list. Among them are insulinlike growth factor, gonadotropins, aromatase inhibitors, selective estrogen receptor modulators, and clomid and other antiestrogens.
• An automatic stay for an initial suspension will be expanded to players disciplined for conduct unrelated to a positive test.
The new joint drug agreement, which must be ratified by both sides, runs until Dec. 11, 2011, when baseball's labor contract expires.