Juan Roman Rocha's Athens team were beaten 2-1 by mid-table Platanias on Sunday in a match which where Panathinaikos' Spanish striker Toche had what seemed a legitimate goal chalked off for offside in the first half.
The result left Panathinaikos in seventh place, 16 points behind arch-rivals Olympiacos.
"Panathinaikos should not be vilified in this way," Antoniadis told Greek radio station SportFM.
"There was a time when match officials took account of Panathinaikos, now they no longer respect the club."
As well as the disallowed goal, hosts Platanias also scored from the penalty spot after another questionable decision from referee Alexandros Aretopoulos.
Any hopes the Greens had of salvaging a point also disappeared when Portuguese midfielder Zeca was dismissed five minutes from full time for picking up what looked a harsh second yellow card.
"We're talking about a man who shaped the outcome of the match," Antoniadis added.
"In the same match he wiped out a regular goal and gave a penalty that only he saw. I do not know even if the president of Platanias would have made that decision.
"Panathinaikos is a great club with a proud history and it should not be discredited in such a way."
Antoniadis's comments followed a brief statement by the club which characterised Sunday's match as a "parody which badly showcased Greek football internationally" while adding that such examples of officiating "threaten the very existence of the club".
Despite the defeat, Panathinaikos have won twice in three games since Rocha replaced Jesualdo Ferreira as coach and Antoniadis believes the side, who face Tottenham Hotspur in their final Europa League group match next week, will continue to improve under the Argentine.
"I'm not worried about the defeat, Panathinaikos are a great team and will find their way," he said.
"We made a coaching change which for me should have been made earlier and Juan has won the confidence of the players and changed the psychology in the dressing room."
The Greek football federation (EPO) has already come under heavy criticism from Panathinaikos president Giannis Alafouzos, who said its decision to approve the restructuring of the Super League midway through the season represented a violation of rules.
The Super League decided earlier this month to change the number of teams to be relegated from three to two, while increasing the number of top flight teams next year from 16 to 18.
Panathinaikos, one of the oldest and most successful clubs in Greek football, appealed the decision via EPO's court of arbitration earlier this month but it was rejected.