According to police, Nix was confronted by the homeowner after crawling through a dog door.
The homeowner kicked Nix in the face and tasered him in the back before another man, Tom Cosgrove, reached through the dog door to pull him out, police said.
Nix and Cosgrove, who also pitches in the Padres organization, were arrested a few streets away from the home.
"We're aware of the alleged incident involving Jacob Nix last Sunday in Arizona," the Padres announced in a statement. "We take this matter seriously and have been in contact with the commissioner's office and local authorities. Due to the ongoing legal proceedings, we will not have any further comment at this time."
The 23-year-old Nix was selected by the Padres in the third round of the 2015 amateur draft. MLB Pipeline lists him as the No. 28-ranked prospect in San Diego's farm system.
Nix was playing for the Peoria Javelinas of the Arizona Fall League at the time of the incident.