Thomas had been arrested in March in Clay County, Fla., for cocaine possession. However, charges were never pursued by prosecutors. According to the Clay County clerk's Web site, the case was abandoned Friday.
Thomas' attorney, Charlie Truncale, said Friday night that he had spoken with assistant state attorney James Boyle earlier in the day and was told the case had been dropped.
"It's over," Truncale said. "I'm so pleased for Marcus."
Thomas, who was dismissed as a senior from the eventual BCS champion Florida Gators in 2006 after repeated positive tests for marijuana, was arrested with his former high school teammate, Bryce Carter, in Jacksonville, Fla.
According to the county Web site Friday, Carter is being charged with third-degree felony possession of a controlled substance.
Truncale said in March that both Thomas and Carter told the arresting officers that the cocaine was in the possession of Carter, who was driving when Carter's truck was stopped for a traffic violation.
However, those statements were not part of the police report. Thomas, Truncale said, recently talked to prosecutors and maintained his story.
"I'm just glad the right thing was done," Truncale said.
The Broncos had no comment Friday night. However, coach Mike Shanahan said in March that the team supported Thomas. Sources have said that if Thomas would have been prosecuted, Denver likely would have cut him.
"Marcus is so appreciative of Coach Shanahan's support and he is happy this thing is over," his agent, Richard Burnoski, said Friday night. "He's looking forward to the future with the Denver Broncos."
Denver drafted Thomas in the fourth round in 2007, moving up to get him at the No. 121 spot by trading a package of picks to the Minnesota Vikings.
Shanahan repeatedly has said Thomas was a top-15 quality pick. He finished last season as a starter and is expected to be teamed with Dewayne Robertson, just acquired from the Jets, in the middle of Denver's defensive line.
Bill Williamson covers the NFL for ESPN.com.