Inter were twice the benefactors of the video review system in the second half at the Stadio Artemio Franchi, with Edimilson Fernandes penalised for a handball in the area before Cristiano Biraghi had a thunderous strike ruled out at the other end.
Fiorentina's luck changed in the final minutes of stoppage time and, after Danilo D'Ambrosio was judged to have handled in Inter's box, referee Rosario Abisso used VAR to confirm his initial decision.
Jordan Veretout kept his composure to secure a share of the spoils in the 101st minute and Inter CEO Marotta did not hold back in his criticism of how the system has been implemented.
"We suffered significant harm," Marotta said on Monday at the Giacinto Facchetti awards ceremony.
"We hope that it's not irreparable in terms of the league standings because it could be really severe.
"This is the biggest mistake since the introduction of VAR.
"The incident took place at the end of the game. Therefore, it was different from the one in the fifth minute when there was plenty of time left to play.
"As a director of football that's part of the Italian movement and the Federation, the main regret is that we've invested a lot in VAR to help referees.
"The aim was not to get rid of all mistakes but to reduce them. It must be used rationally. We're now faced with a situation where objectivity has been confused with subjectivity. I cannot help but remain disappointed and stunned.
"D'Ambrosio's action is objective and what's happened is incredible."
Luciano Spalletti's side were behind after 17 seconds when Stefan de Vrij turned Giovanni Simeone's flick into the back of Inter's net.
Matias Vecino restored parity before Matteo Politano hammered home – Ivan Perisic extending Inter's lead from the spot after the interval.
But after Biraghi's effort was disallowed, Luis Muriel's sensational free-kick set up a grandstand finish, with Inter wilting under the Fiorentina pressure, and the Nerazzurri are now just two points above fourth-placed AC Milan.