He was suspended for 25 games by the NHL for a cross-check to the head of Vancouver Canucks forward Ryan Kesler during a game on Oct. 10.
Boulerice was assigned to the Phantoms last Wednesday, two days after the Flyers placed him on waivers. The ineligibility ruling means he will miss 25 AHL games.
"Over the last several seasons, the American Hockey League has established a strict disciplinary standard relative to violent play," AHL president David Andrews said in a statement. "We strongly support the National Hockey League's recent decisions relative to targeting the head of an opponent.
"In determining his eligibility date, it was taken into account that this is the second time in his career that Mr. Boulerice has been assigned to the AHL while under a lengthy suspension in another league."
In 1998, Boulerice was suspended for one year by the Ontario Hockey League for a violent stick-swinging incident. He went to the AHL the following season and was ruled ineligible until mid-November.
Boulerice apologized to Kesler, who was not seriously hurt. The NHL's 25-game suspension matched the longest punishment handed out by the league for an on-ice incident.
Boulerice, a 29-year-old native of Plattsburgh, N.Y., has 319 penalty minutes in 167 career NHL games.
According to league bylaws, a player under suspension in another league who seeks to play in the AHL while under that suspension will have the disciplinary matter independently reviewed by the AHL president, who may in his discretion deem the player ineligible.
Boulerice's AHL eligibility does not affect the terms of his NHL suspension.