Riding high on the back of their mid-week Asian Champions League victory over Chinese giants Guangzhou Evergrande, Coach Graham Arnold was forced to shuffle his line-up.
David Carney, Seb Ryall, Jacques Faty and Rhyan Grant were all suspended while Alex Brosque was out with a hamstring injury.
Sydney FC had the better of the opening period, Filip Holosko was proving a handful deep in attack and his scything run in the 39th minute forced a cynical tackle from City skipper Patrick Kisnorbo, who was shown a yellow card by referee Jarred Gillett that could have easily been a red.
City opened the scoring just before half-time when a hopeful counter-attack ended with the ball in the net thanks to the brilliance of Fornaroli and play-maker Aaron Mooy.
After bringing down a long hopeful pass, Fornaroli bamboozled Aaron Calver before passing to an over-lapping Mooy who's calm cross was volleyed home by the Uruguayan.
Harry Novillo returned to City's starting line-up after his club-imposed two week suspension and in the 70th minute played through Fornaroli who showed his class with a cool turn and finish.
By the 80th minute a limp Sydney FC had seem to have given up on the match when Michael Zullo's cross found Fornaroli at the back post who had no issue scoring his 20th goal of the campaign.
Fornaroli becomes the first player in A-League history to score 20 goals in the regular season, while Melbourne City move within three points of Brisbane Roar and Western Sydney who sit in second and third respectively.
