A state prosecutor told reporters that Herrera's girlfriend did not want to proceed with the case, leading to the decision to dismiss.
Herrera must complete counseling within 60 days as a condition of the dismissal.
Major League Baseball said afterward that Herrera will remain on administrative leave through Friday, when his case will be reevaluated.
Phillies manager Gabe Kapler said the team will await the completion of MLB's investigation.
"This is still in the league's hands," Kapler said before Wednesday night's game at Atlanta. "Until their investigation is complete, I'm not prepared to address it."
Herrera had been accused of domestic assault against his girlfriend on May 27 at the Golden Nugget Hotel and Casino in Atlantic City. Officers said they found the 20-year-old woman with "visible signs of injury to her arms and neck that was sustained after being assaulted by her boyfriend."
Herrera, 27, had been facing charges of simple assault and knowingly causing bodily injury.
"We believe that the complete dismissal of the misdemeanor charges was the right result," Herrera's attorney, Thomas Calcagni, told reporters.
Following the arrest, Herrera was placed on administrative leave by MLB. He has not played for the Phillies since May 26.
The Associated Press contributed to this report.