Empoli equalised in the 77th minute of Monday's 1-1 draw , with Massimo Maccarone's header from a corner deflecting off Tonelli's hand and into the net.
Despite mass protests from the home side, referee Angelo Cervellera let the goal stand and Empoli extended their unbeaten league run to five matches, while Genoa failed to build on their impressive win at Parma before the international break.
Genoa took the lead with a blistering half-volley from Andrea Bertolacci after 13 minutes, the midfielder smashing home from the edge of the area after Alessandro Matri had half-controlled Edenilson's long ball forward.
But Genoa displayed disappointing profligacy at the Stadio Luigi Ferraris, just three of their 13 shots hitting the target.
And they were punished in unconventional fashion as Tonelli diverted Maccarone's header in at the near post with his right hand, meaning that Genoa have won only two of their first seven games in Italy's top flight.
The draw takes Empoli to 13th in the standings on seven points while Genoa sit 10th with nine to their name.
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