Tonelli inadvertently deflected Massimo Maccarone's header into Genoa's net with his hand in the 77th minute of Monday's Serie A fixture, cancelling out Andrea Bertolacci's scorching first-half strike for the home side.
However, Gasperini was more aggrieved by referee Andrea Cervellera's decision not to award a penalty, when Antonelli was fouled in the area by Maccarone - only for the linesman to have incorrectly flagged for offside.
"According to the referee, he didn't see the Empoli goal. If he had seen it, he would not have given the goal," Gasperini said.
"Penalty on Antonelli? There was, but the referee has whistled offside. But that [offside] was not there. So it was a penalty to give."
Gasperini also hit out at Genoa's fans who booed him and the team following their draw.
Genoa have won just two of seven games this season to sit 10th in Serie A with nine points, four adrift of the UEFA Europa League qualifying berths.
Gasperini said Genoa's supporters are unjustifiably negative - although the club have not won a top-flight trophy since they claimed the Coppa Italia in the 1936-37 season.
"Here at Genoa, there is too much negativity, it's a different environment from that of years ago," Gasperini said.
"The fans have lived through difficult times but this is a team that deserves to be supported and not only attacked.
"Some people don't deserve to support a team, because they're incompetent and ditch players of a good standard to promote others who haven't played."
The 56-year-old coach added: "We are a team that are appreciated by most of our fans but we have to raise our voice against a minority.
"I hope that anyone who loves Genoa has a better attitude, because anyone who wishes to destroy a team should not follow football.
"In recent years, Genoa became more famous for their jerseys being delivered to fans during matches.
"We're doing a lot to add value to this team. The president has worked through many obstacles. I think that even our most ardent fans deserve better."
