Hennepin County District Judge Peter Cahill also let stand all other charges against Chauvin's co-defendants.
Cahill ruled that while third-degree murder is applicable when a defendant's actions could have harmed "others," prosecutors are accusing Chauvin in the death of just one victim, Floyd.
"The language of the third-degree murder statute explicitly requires the act causing the 'death of another' must be eminently dangerous 'to others,'" Cahill wrote.
Minnesota Attorney General Keith Ellison, whose office is handing the case, downplayed the dismissal.
"The court has sustained eight out of nine charges against the defendants in the murder of George Floyd, including the most serious charges against all four defendants," Ellison said in a statement.
"This means that all four defendants will stand trial for murder and manslaughter, both in the second degree. This is an important, positive step forward in the path toward justice for George Floyd, his family, our community, and Minnesota. We look forward to presenting the prosecution's case to a jury in Hennepin County."
Mark Osler, a former federal prosecutor who is a law professor at the University of St. Thomas in Minnesota, said losing a lesser included charge is at least a small setback for the state. Any jurors who might feel uncomfortable convicting Chauvin of second-degree murder now have one fewer avenue to convict him of a serious offense.
"They wouldn't have charged it if they didn't want it going in front of a jury," Osler said. "You always want to give options to a jury."
Chauvin's attorney, Eric J. Nelson, could not be immediately reached for comment Thursday.
The judge let stand all charges against three other former Minneapolis officers in the case, J. Alexander Kueng, Thomas Lane and Tou Thao, who are all charged with aiding and abetting second-degree murder and aiding and abetting second-degree manslaughter.
Floyd's death sparked protests around the country and the world against police brutality and systemic racism.