Jestyfer Henriquez, 25, of the Bronx was arrested and charged with assault on Friday.
Amr Alzabibi was working behind the counter at Stadium Gourmet Deli on East 161st Street in the Concourse section on May 29 when two customers became enraged in a dispute over a food order around 5 a.m.
Video released by the NYPD shows two men attacking Alzabibi by throwing the fruit at him.
Alzabibi suffered a broken jaw, along with fractures and a cut to his face. The suspects fled the scene.
"I know it sounds funny, an avocado," he said. "But the avocado, the weight and the speed, fractured my face and caused me double vision, blurry vision, and I'm not sure if I'm going to have to deal with this for the rest of my life."
The first suspect, Brad Gomez, 28, of the Bronx, was arrested Thursday and charged with assault. Detectives were able to identify him after the video was released earlier in the week.