Jarrod Bowen scored a last-minute winner to end a 43-year wait for a major trophy for the east London club.
It was an ill-tempered affair both on and off the pitch in Prague with sixteen arrests made prior to kick-off after Fiorentina supporters attacked a group of West Ham fans.
Czech police confirmed three people were injured in the incident, with one police officer attacked.
Hammers fans following the game clashed with riot police in the Czech capital after police officers tried to confiscate a flare from supporters gathered in the Old Town area of the city.
Speaking to Italian media after the game, Commisso said: “There have been episodes on the pitch where the referee had to make the difference.
“[Luka] Jovic came out with a broken nose, Biraghi with a cut on his head.
“I spoke to the president of the Premier League, those of West Ham are animals in the way they treated ours.
“It’s not right.”