The bats were taken from the Chicago Cubs' locker room during the game against the Tampa Bay Devil Rays on Tuesday night. Cork was found in Sosa's bat when it shattered after he grounded out in the first inning of the Cubs' 3-2 victory.
"The bats were clean and had no foreign substances in them," said Sandy Alderson, executive vice president of baseball operations in the commissioner's office. "That is consistent with Sammy's explanation of the incident last night."
Sosa said he accidentally pulled out a bat he uses to put on home run displays for fans in batting practice. He has had dozens of bats break in the past few years with nothing suspicious found.
He was in the lineup for Wednesday night's game against Tampa Bay.
"I stood up yesterday like a man and took the blame," Sosa said. "But the media today, they've got me up there like I'm a criminal."
Sosa could face a suspension of up to 10 games, but Alderson said the decision will be made by Bob Watson, baseball's vice president in charge of discipline.
Watson was expected to arrive in Chicago by Thursday morning and will conduct interviews at the ballpark.
Alderson said commissioner Bud Selig was "very concerned."
"He has strong personal affection for Sammy," Alderson said. "At the same time, he instructed his office to conduct a thorough investigation."
At a news conference after the game Tuesday, Sosa said the use of the bat was a "mistake. I know that, and I'm sorry."
The world-renowned Cubs player says use of the bat was an accident. Sosa explains that this bat is one he uses for batting practice to put on a show for fans, but in this case, he grabbed the wrong bat when game time arrived.
The Cubs had runners at second and third when Sosa broke his bat with a grounder to second that at first appeared to drive in a run.
Cork inside a wooden bat is thought to help players hit the ball farther and is against baseball rules. Several players have been caught using altered bats in the past, including Albert Belle, Wilton Guerrero, Chris Sabo, Billy Hatcher and Graig Nettles. All were suspended.
But Sosa is a far bigger star, 17th on the career list with 505 homers, and he gained international prominence in 1998 during his home-run battle with Mark McGwire.
"Unfortunately, it's a dirty mark, when you consider all he's accomplished," Yankees manager Joe Torre said. "It's really unfortunate for the game. Everybody's scratching their heads right now. ... It's embarrassing. He's too good of a player. It's too bad."
But how can one of the game's foremost power hitters repair his reputation or silence the doubters?
"It's going to be tough. Some fans are probably not too happy about it," said Sosa. "I've got to deal with that... I know that I lost the fans and they have been great to me. It's a mistake, and I take the blame for it."
Seattle second baseman Bret Boone said Sosa's career shouldn't be judged on this one incident.
"I just hope it doesn't taint what he's done," Boone said. "Corked, not corked, he's got as much power as anyone in baseball. He's probably got as much power, outside Mark McGwire, as anyone in history. It's probably embarrassing for him... Pitchers cheat all the time. They scuff balls, use pine tar. I've never used a corked bat, not even in batting practice. If I was guaranteed I wouldn't get caught, I probably would."
Sosa, a six-time All-Star who reached 500 career homers earlier this season, hasn't had a homer since May 1 and his power numbers have dropped drastically since he was beaned April 20 by the Pirates' Salomon Torres.
He has just six homers this season and 24 RBIs, while batting .285.
Sosa has the most 60-homer seasons (three) in major league history, hitting 66 in 1998, 63 in 1999 and 64 in 2001.