The fiery Italian labelled the official a "clown" and "loudmouth" on his way to crashing out of the tournament.
Fognini's defeat of Britain's out-of-form defending champion Andy Murray earlier this week raised hopes he could finally make it past the third round for the first time in his career.
But in a 1hr 19min clash that drew whistles from his own fans on centre court, the fiery Italian, ranked 29 in the world, was brought crashing back to earth by the clinical game of 20-year-old German prodigy Alexander Zverev.
Fognini swore at chair umpire Mohamed Lahyani at the end of a match which saw the Italian smash his racquet on the ground on several occasions and kick a linesman's chair.
Lahyani, a Swede of Moroccan origin, soaked it all up. He is already popular with tennis watchers following his officiating of the combustible Wimbledon final in 2013 that saw Murray end Britain’s 77-year title drought.
Fognini also labelled him a "clown" and "loudmouth" on his way to crashing out before the business end of the tournament in Rome.
Zverev, the 16th seed who is the youngest player in the ATP top 50, will meet the winner of the clash between Tomas Berdych and Milos Raonic, to be played later Thursday.
With Murray out, Rafael Nadal is heavily tipped to secure an eighth Rome Masters crown.
The Spanish fourth seed, fresh from victory in a Madrid Masters triumph that saw him cruise past Serbian nemesis Novak Djokovic in the semis, will meet American Jack Sock in his third-round match later.
Nadal is enjoying his best tennis on clay for the past two seasons but played just three games of his second-round match with Nicolas Almagro on Wednesday before his fellow Spaniard retired through injury.
Djokovic is in action later against unseeded Spaniard Roberto Bautista.
In the women's tournament Venus Williams overcame determined Briton Johanna Konta to win their third-round clash 6-1, 3-6, 6-1.
In the absence of sister and defending champion Serena, she will now meet Germany's Julia Goerges or Spain's Garbine Muguruza on Friday for a place in the semis and a possible match-up with Czech second seed Karolina Pliskova.
Russia's Svetlana Kuznetsova, the seventh seed, won't be going so far after she exited following a 2-6, 7-5, 6-4 defeat to Australian qualifier Daria Gavrilova.
Gavrilova will meet the winner of the match between Dutch 15th seed Kiki Bertens and unseeded Russian Ekaterina Makarova.