Judge Elizabeth Pollard Hines said the prosecution did not prove beyond a reasonable doubt that Furman had committed illegal entry, assault and battery, or domestic violence.
Furman declined to comment after the verdict.
Furman was arrested Feb. 11 and charged with the three counts after an incident at an Ann Arbor residence.
Three witnesses had testified Monday, giving their accounts of what happened that night. Furman's attorney, Gerry Mason, explained Thursday why he didn't have many objections during their testimony.
"When your client is innocent," Mason said, "let it all in."
The Washtenaw County prosecutor's office had offered a plea on the domestic violence charge, but that likely would have kept Furman -- who was suspended -- off the football team.
Mason said his client was the one who wanted to go to trial.
"My goal wasn't to win the trial," Mason said. "It was to get a clean record."
Pollard Hines, in her summation, said Furman "shouldn't have gone in" the apartment, but the burden of proof -- that he entered illegally -- wasn't met.
Michigan coach Brady Hoke made a brief statement after being notified of the case's conclusion.
"We were informed of the court's decision today," Hoke said. "Josh's status with our football team is still being evaluated at this time."
Prosecutor Patricia Reiser declined to comment after the trial.